Replying to Mac and Converting .MOV (Quicktime)

I work in After Effects and when I export a comp as a .MOV file, I'll go to open it and my Mac will convert it before playing. Yet the file appears to still be a .MOV file it just says (converted) before the file tag. So why does it do this? And if I want to use the file back in a larger After Effects project do I use the original MOV file or the converted one. They are both Quicktime files so I'm just confused.