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I have been using Thunderbird for years in the following manner (now it's Thunderbird 17.0 on Windows 7):

I offload my IMAP emails to my local inbox weekly, then apply hundreds of message filters to said emails in order to move and store them into a few hundred subfolders. It's always worked like a charm - until recently.

Now, after I apply the message filters, the emails get moved but they are destroyed in the process - bodies are scrambled up, with bits and pieces of other emails or they are simply blank!

How do I fix this?

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I suggest that first try reinstalling TB 17.0 -- what you describe sounds very uncommon so perhaps something is corrupted. – martineau Dec 20 '12 at 2:05
A) "until recently" can be pretty anything. Can you be more specific (I know it can be hard, but often a guess is better than nothing). B) could you more specifically describe how the messages are garbled? (real sample would be best, if policies allow it) – Alois Mahdal Dec 20 '12 at 3:15
Maybe the simplest option: Too large mail folders ... broken index database in some of them? Make a copy of your profile folder as a backup and then try rebuilding the index files for each folder ... – ernestopheles Dec 20 '12 at 8:03
Thanks for the feedback. I know how to make a profile back-up using MozBackup but how do I "rebuild the index files for each folder"? – Adrien Dec 20 '12 at 21:25
The emails become garbled with a lot of code, like this: </div> <div style=3D"color: rgb(0, 0, 0); font-family: 'Trebuchet MS', sans-serif; font-size: 12px; "><br> </div> <div style=3D"color: rgb(0, 0, 0); font-family: 'Trebuchet MS', sans-serif; font-size: 12px; "> <div style=3D"font-family: Calibri; font-size: – Adrien Dec 20 '12 at 21:27

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