Rendering LOSES Video -Please Help Desperate College Student

I am in desperate need of help, as no one around me has ever had this problem:
When I render select clips Final Cut loses that video clip and cuts out the footage. The clip is then replaced with video that was on either side of the original clip, like taking a curtain and closing it. I can't retrieve the video after I render it.
I would simply return to my raw footage to try and salvage the project, but to get the sequence I have now took about 24 hours of scouring 3 hours of film for short clips.
This has never happened to me before, and the problem occurs only with select clips that seemingly have nothing in common.
Also note, the audio is not effected by this.
Any advice is welcome, this project was due 11 hours ago :P

I have.
The only thing that seems to be causing it is when I use the "flop" video filter on the clip. Then, when it renders the original clip i had picked out has been squished out or something. I have also tried linking it and telling Final Cut that it is "synced"

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