Are you saving the MOVs alongside the original AVIs?
I'd try saving your project as an After Effects XML file (File > Save As > Save a Copy as XML...). Open that AEPX file in a text editor, then do a search and replace operation, changing all ".AVI" to ".MOV"
Re-open the AEPX in Ae, and it should connect to the MOV media instead of the original AVI media.
Walter Soyka
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