Deleted emails re-appearing in inbox (thousands at a time)

I haven't found an answer to this in previous threads, but if I've missed it, please do point me in the right direction.
I'm using Mail 1.3.11 on my iBook G4 (OSX 10.3.9). My account is linked to a POP Yahoo mail account and a couple of others.
I'm having a problem that re-occurs every so often. After trying to be good and clearing out my inbox, Mail will (without prompting or anything) start 'downloading' all the emails again--though i don't think it is really downloading them from the Yahoo account. Hundreds, if not thousands, of emails re-appear in my inbox. I think it is dredging them up from some file on my computer; it reads "indexing 1 of 4577" etc. and the process also takes a while and makes the computer slow.
this has happened about 4 times in the last few months and it's quite disheartening! I've made a backup of my mail folder already after reading a few posts on similar-sounding problems.
any guidance would be very much appreciated!!
BA

Yes, thank you for your reply. I went through my Inbox on my Mac mail application (using the viewer window), and then selected all the emails i didn't want anymore, then clicked the delete key. I'd select a few at a time, then delete, etc.
At one point I worried that leaving these messages in my inbox on my Yahoo account would be the root of the problem; however, I did at one point move all of those messages to a separate folder so they are no longer in my Yahoo inbox, and the problem has occurred since I took this measure.
Let me know if I am not being specific enough--happy to elaborate.

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