I used to work with a SONY Z7U fairly often on MC3. My workflow back then was to just do a “fast import” off of the Z7U hard drive with color import levels at 601/709. I would do a general search for all .m2t files, pick them accordingly, and then import all of them. So thats something to try, I cannot say what the best 5.5 workflow is.
I cannot solve your issue as to why pieces of your footage is missing, do you mean sections of individual clips? Or whole clips altogether?
“Where that light source is coming from?”
“The same place as the music.”