Trouble with Sony Fx6 and Fx3 Metadata Timecode Shift Danger Stripes

We are editing on Sony Fx6 (MXF) and Sony Fx3 (mp4) media (4K) with sound in the clips (not external).

Fx6 (8 channels/24bit) Fx3(1 channel/16bit).

The footage was delievered only by single clips, not the full CARD Memory Data and Folders (as ususal).

After successfully editing a first rough cut and shutting down the system, we end up having danger stripes in 90% of our clips in the timeline. The fault clips then always start with the very beginning of each clip.

We try to fix it multiple ways:

1. Putting Media offline and re-linking (Deselect "Align Timecode")

2. Putting Media offline and re-linking (Select "Align Timecode")

3. Now we started to use Media Encoder to produce new video clips with reset Timecode (00:00:00)

But option 3 is very burdensome. We have to start the edit all over.

We suspect it has someting to do with the Metadate/Timecode of the clips.

Is there any idea how to save the project?

Thanks!