I am not sure if this would work for you. I have five email accounts that I want to keep separate, e.g. Personal, Business, etc. I set up five Pmail folders, each having the Program and Mail subfolders. Then I mapped five "network" drives to these folders. I have an shortcut icons on my Desktop to access each email account.

Pegasus Mail is with me for about 20 years now and I never had any real problems with it. Now I have some dilemma and I'm looking for the answer to choose the best possible way to handle it.

At the beginning of 2014 my system (including HDD) went out of order and I needed to get on another PC. Luckily: I had some data backups. Unluckily: they were a few months old (from 2013). At that time I was not able to recover mail database from my HDD so I decided that, for the time being, I'll use webinterface of my mail provider as I discovered it was quite simple and easy to use. And as every "temporary thing" it prolonged to two years...

I would probably still continue to open mails in my browser but recently whole webinterface got a change. Now it's a pain to use for me as I lost some options which were important for me (like any kind of mail sorting and advanced search). As far as I know (according to my mail provider) there is no way I can go back to my previous webinterface so I decided to go back to Pegasus Mail.

Now, I have these three things:
#1. PMail database on my DVD in backup - until the 2013
#2. PMail database on my old (out of order?) HDD - until the start of 2014
#3. mails in my webinterface - since the start of 2014

Two options to handle this situation:
#A. use #2 database and download #3 mails - that way I would have my whole mail history in one place
#B. use #1 database and download #3 mails - that way I will miss my mails from between 2013 and 2014 (a period of few months)

Option #A is clearly better one but the problem is I still don't have the access to this old HDD so #A is not really possible at the moment...

My question: when I follow #B and then, at later date, I will be able to somehow recover #2 - will I still be able to add only these missing mails without duplicates from #2? Is there some easy way to do this or will that be some tedious process (like searching/deleting all duplicates from #2 before merging or even something worse)?

Or maybe the best/safe way for now would be just to download #3 and wait with full mail history merge till I get confirmed "yes" or "no" on #2 recovery? In that case I suppose that merge of downloaded #3 with #1 or #2 at later date will be still possible? Here is the problem: I don't know how quick I will be able to get such yes/no "recovery possible" confirmation...

One more note: my #1 backup and (probably) #2 database were used with Pegasus Mail v.4.51 (I had some troubles with installation of the newer one).

Here's my two cents...

You are correct that trying to merge #1 and #2 backups will be difficult because of all of the duplication.  If you can recover #2 (the one on the HDD), you may be able to copy it to the new system and use it.  Whether this is possible will depend on the location of that installation.  If is was to C:\PMAIL with the mailbox directory as C:\PMAIL\MAIL then you have a good chance of this working.  An upgrade is strongly suggested and may be required depending on the SSL version requirement of your mailbox host. 

If the original install was to anywhere inside of the \Program Files directory (which was common on Win98 and WinXP) then a direct copy to the new system will not work.

So, I suggest waiting until you determine whether the HDD is recoverable but if that wait is not practical then do a clean install of Pegasus Mail and we can then help with recovery of mail data from whichever backup you can recover from.

Could you not use the 'Add Mailbox to List'?

Place the e-mail folders from DVD etc in a separate folder from your main Pegasus mailstore.

My Documents\Pegasus_DVD

My Documents\Pegasus_old_hdd

This way you can 'mount' the archive/old mails into Pegasus view the structure and messages. Use filtering/searches to copy from the added mailbox into the current mailstore.

 Pegasus Manual Chapter 5 (pg48) does have more information.