Brian, you prompted me to do some experimenting, using new test messages in new test folders and with new simple annotations - so results are clear. I checked what was happening with files in the user Pmail/Mail directory each time. The results are:

- (Re your query) Moving a previously annotated message - now with the annotation absent - back to the new mail folder from a temporary folder does not re-establish links to the orphaned annotations.

-  Moving a still-annotated message back to the new mail folder from a temporary folder works fine and it appears there complete with the annotation.

- Green dots, indicating the existence of annotations, work exactly as one would expect they should i.e. once a message gets an annotation the green dot exists until the message is finally deleted, including in copies and following moves between folders.

-  Deleting a message with linked annotation from the new mail folder (i.e. a .CNM) or from another folder (i.e. a .PMM/.PMI) deletes any associated annotation, without leaving orphaned .PMN annotation files behind i.e. exactly as one would expect. (Note: To be clear, I did no direct editing of Pegasus files using Windows; always using Pegasus menus).

- Deleting a message that has an orphaned annotation 

(i.e. a .CNM or .PMM/.PMI exists as well as a previously associated .PMN in the user's Pmail/mail folder) - leaves the associated orphaned annotation behind.

- Re-indexing a test folder after moving a message out to the new mail folder - or to any other folder - caused the message to reappear in the test folder, complete with green dot but without the original annotation. It also exists in the folder to which it has been moved, but in that case the annotation is still attached (unless re-indexing has also occurred in that folder).

- Recovering deleted space, without subsequent re-indexing, has no impact on annotations. Recovering space and then re-indexing seems to prevent a moved message reappearing, so the question of associated annotation is irrelevant.

- Whenever an annotated message is moved (without re-indexing), its long Hex .PMN filename is changed.

- The impact on annotations of moving messages between folders is the same as copying messages between folders (as one might expect).

- Searching for references to the names of annotation files throughout the user's Pmail/Mail directory (i.e. checking in file contents), brings up no relevant results. However, as a link clearly does exist originally between the message file and its annotation, which was when I checked then I think Brian's conclusion that the link is encoded somehow in the relevant files.

Overall conclusion: The potentially very useful note-taking facility of annotations is fatally flawed by (a) the fact that re-indexing breaks the link between message and annotation and (b) the absence of any facility to remake these important links and indeed the lack of information on how to identify which orphaned annotation file belongs to which message file.

As an afterthought, the reappearance of previously deleted or moved messages upon re-indexing should ideally be addressed at some stage.

At some stage in the last days/weeks all my annotations became unavailable. I count approx 93 messages with green dots showing while there are some 220 .PMN files in my mail folder but no annotations actually now appear when 'edit' is selected (i.e. the box is blank). Some checks of .PMN content (including time stamps) against the message dates show there seems to be alignment with the green dots, though opening messages with green dots always results in blank annotations. I have checked forum messages and found I cannot expect to identify linkages between .PMN files and corresponding .PMM/.PMI files, which would have been a help. I have also logged into the PC under each user name in turn, opened Pegasus and opened green dot messages - but the results are always blank annotation boxes.

All but 13 annotation files are in the 'new' long name Hex format, with the oldest going back to 2000. I am using Win10 and annotations were working successfully on this until recently.

I am not clear why the green dot messages are so much fewer  than the .PMN files, unless annotations always remain as left-overs from deleted messages. Also, I am hoping someone here has ideas about how to again link the PMN files to the relevant .PMM/.PMI messages; otherwise trusting important data to annotations seems to be too risky.

Any clues gratefully received as there is useful/essential stuff (e.g. Password clues!) in many annotations but these are obviously only useful when linked to the original messages.

No answers so far! I guess the mechanism used by annotations to link to their corresponding .PMI/.PMM files is something of a mystery to users at this stage. In any case, if annotations can vanish even though the green dots showing they were once present remain in place, then they are worse than useless. Important information contained in these annotation notes is too difficult to access when it only remains in any one of a collection of orphaned .PMN files in a user's Mail folder.

[quote user="Patrick Walsh"]

At some stage in the last days/weeks all my annotations became unavailable. I count approx 93 messages with green dots showing while there are some 220 .PMN files in my mail folder but no annotations actually now appear when 'edit' is selected (i.e. the box is blank). Some checks of .PMN content (including time stamps) against the message dates show there seems to be alignment with the green dots, though opening messages with green dots always results in blank annotations. I have checked forum messages and found I cannot expect to identify linkages between .PMN files and corresponding .PMM/.PMI files, which would have been a help. I have also logged into the PC under each user name in turn, opened Pegasus and opened green dot messages - but the results are always blank annotation boxes.

All but 13 annotation files are in the 'new' long name Hex format, with the oldest going back to 2000. I am using Win10 and annotations were working successfully on this until recently.

I am not clear why the green dot messages are so much fewer  than the .PMN files, unless annotations always remain as left-overs from deleted messages. Also, I am hoping someone here has ideas about how to again link the PMN files to the relevant .PMM/.PMI messages; otherwise trusting important data to annotations seems to be too risky.

Any clues gratefully received as there is useful/essential stuff (e.g. Password clues!) in many annotations but these are obviously only useful when linked to the original messages.

I spent a good bit of time trying to determine the link between the message and its associated .PMN file but was unable to do so, as you have already noted.  I find it interesting that each time an annotation is edited the date/time stamp on the associated .CNM file is changed to match that of the .PMN file but I find nothing in the .CNM file that links the two.  I have found that changing the name of the .CNM file breaks the link so perhaps the filename is somehow encoded into the .PMN filename.  If so, that is of no help in fixing the problem unless someone can explain exactly how all this works.  It certainly doesn't help once a message is moved into a folder (my testing was limited to new messages).

I did figure out that the green dot is the result of the "Has associated annotations" flag being in place.  Not much use to have that indicator when the link to the annotation file is broken. It seems odd that you can manually set that flag even when there aren't any annotations.

FWIW, in my tests the .PMN files was always deleted when the associated .CNM file was deleted. 

Hmmm! Although my issue is with annotation linkages to messages in folders, the underlying problem is no doubt the same as yours i.e. how the existence of annotations is known by Pegasus. Your reply reminded me that at some point before I noticed my annotations were 'missing', I had taken time out to go through all my folders recovering deleted space and re-indexing. I had forgotten about this but your mention that changing .CNM filenames (= 'deleting' the previous file, in one sense) causes annotation linkages to be lost makes me wonder if somehow that tidying up of my folders caused the problem. It could explain why the loss of linkages was total  rather than some individual failure - though still leaving the question of why ANY annotation linkages were lost by a house-keeping exercise (if indeed that was the cause).

There is a note at the bottom message properties window that makes reference to the properties potentially being lost if the folder containing the message is reindexed or otherwise modified.  It now appears that annotations should be included in this warning but the fact that reindexing can be harmful is very concerning.

Have you tried moving an annotated message back to the new mail folder to see if it re-establishes its link to the annotation?