Editing with Canon 5D Mark II Problems

Hello fcp experts,
I shot a short film on 5D and I did not know that I should convert the raw files to Apple ProRes 422 in Compressor and then edit it on final cut pro.
I already edited the raw files in fcp. and I started adding fades and outline texts. then I rendered them and exported it. That's when I realized that the color of the video changed whenever there was subtitle or fades.
Is there any way to fix this or do I have to convert all the files to Apple ProRes 422? (I did start) Is there any short cut to this?? Please help!!!

sorimsanim wrote:
I followed this guideline I found online and it said to set in and out points on the raw files in Compressor.
I've never heard of this being done in any of the conversion workflows I'm aware of, and it seems like a waste of time. The amount of drive space you'll save will be negligible - if saving space is the reasoning behind it. Reconnect to the ones without in and out points.
+And could you tell me the exact settings after conversion? It should be Apple ProRes 422, right?+
If that's what you converted them to, then yes.

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