I believe Clip Browser 1 had a serious bug when creating new BPAV folders. I reported this to Sony some time back. It was fixed in Clip Browser 2.
I wouldn’t be surprised that Clip Browser 1 created defective BPAV folders. By “eye” they look fine but apparently were missing crucial data that XDCAM Transfer needed and therefore wouldn’t recognize the clips.
Unfortunately by you can’t tell which BPAV folders are defective.
While I had no major issue splitting BPAV in CB1 I had not attempted to combine BPAV. I did find that when I imported an MP4 and created a new BPAV the the BPAV CB1 created was defective. I have a hunch that CB1 may also be creating defective BPAV folders when combining. If I understand you, you combined BPAV in CB1 and I think that is the root of the issue.
ClipBrowser2 IS able to take the MP4 and create new viable BPAV folders. It creates new meta data but, in the end, you’ll have clips you can use with XDCAM Transfer to rewrap as MOV for FCP.
Depending on the results of the next question I’ll make a suggestion.
Using CB2, can it see all the BPAV folders and the clips in them?
If so, you may attempt to split them into separate 8GB BPAVs
If CB2 can NOT see all the BPAV folders and their clips then import each individual MP4 (Use CB2 Import feature to import individual MP4 clips) and then create new BPAV under 8GB. Doing this you’ll be loosing your meta data but the new BPAVs should work.