I have 930 .pmm files with a total size of 28 gb.
Messages in the New Mail folder become invisible seemingly at random. But if I search for them with ctrl-f pmail finds them and tells me that they are in New Mail folder.

I have tried to move all the messages into a temporary folder and then moving them back into the New Mail folder. But then the missing messages cannot be found anymore at all.

Any ideas ?

How many messages do you keep in your new mail folder (or CNM files for that matter)? There's a limit beyond which Pegasus Mail stops parsing the new mail folder for messages automatically for faster operation at opening, it's said to be at around 800 messages.

Just to clarify. There actually is no New Mail Folder. Messages in the Mail Folder that have not been moved to a different folder exist and Individual .CNM messages. So there is no .PMM/.PMI file for the new mail folder.

Has been noted that having a large number .CNM files in the directory can cause a slow down of opening Pegasus, since it has to open each file one by one, rather then just opening the PMM file with the already created PMI index file.
I don't recall and exact number of CNM files.

Not sure about messages disappearing. What comes to mind. With a large number of CNM files existing, the filter rules you have might not have process them. But when you moved them to a folder, and then back to the indiviual CNM files, the filter rules may have been able to process them as they were being created, and moved or processed them as rules. But that is only a guess. Do you have rules that either move of delete messages. Have you tried scanning all mail folders for a specific message content that seems to be gone. If you find one of the messages, then check you rules to see if any would have processed it.

I don't leave messages in my New Mail folder. My rules move about 80% to specif folders, were I then look at them. Those left in the New Mail folder, and mostly junk mail, or messages not part of lists, and I move them to folders.

Good Luck.

I have currently 5400 .cnm files. PM shows the same number of New Mail messages.

I don't think that this problem is related to the 800 messages that you mention because most messages do not disappear. Also, the messages do get displayed initially, but at some later point - maybe later that day they vanish. And I only find out because the next I say "hey, wasn't there a message from Peter yesterday? where is it ? what happened?"

I only mentioned the .PMM files because I had seen a message that says that Pmail can only handle up to 2 gb in .PMM files. My impression is however that this is not really relevant to my problem.

I have only very few rules and none of them seems to be able to cause such a behavior by Pmail. I also checked the target folder, and the invisible messages are not there either.

Your problem will go away once you reduce the new message count to below 700. 5400 .cnm files (eg: new mail folder entries) is WAY too many. It is not designed to handle anywhere near that many. Michael stated around 800. I advocate staying below 700.

Each time the new mail folder is opened, an attempts is made to parse each .cnm file, obtaining the information it needs to populate the new mail folder content, while processing all unread ones through new mail filters. A new message count that stresses Pegasus Mail's capability manifests itself in two ways, one is that newly arrived messages may not appear, and the other is that random messages fail to appear. It does not manifest itself such that it only displays 700-800 messages. It's behavior just becomes erratic.