This happened to me with BMCC when I purchased SSD cards that weren’t as fast as was claimed and didn’t realize that the flashing “REC” meant I was dropping tons of frames. Lesson Learned.
I was able to fix the footage using Capture One pro, and processing all of the files as a jpeg sequence. Then, the sequence was uploaded into After Effects as Jpeg Sequence –> Force Alphabetical. Then, I used Twixtor to extend by 30% since roughly 1/3 of frames were missing. The result, as you would guess, was not perfect, but it was passable since each clip was only going to be used for a second or two at a time.
It’s time consuming, as you would expect.
Hope this helps.