I'm encountering a problem I have never seen after 10 years of using FCP (now Legacy).
Several clips I have in a project have their timecodes zeroed. (00:00 ...) Many of these clips went through merged clips (both the merged clips and the originals are zeroed). They are all Red footage transcoded into Prores (though I don't think this is the issue. The bizarre thing is that if I create a new project and import the same media into final cut they also come with their timecodes zeroed-out. But if I bring those media into Premiere, for instance, the timecode is still there. Furthermore, if I trash final cut pro preferences, and them bring the media back into a fresh project, the timecode is back there. So, it seems the "corruppted project" where the timecodes zero out create a kind of corrupted link between FCP itself and those clips. The worst part about this is that I first encountered the problem in a machine using Sierra and FCP 7.0.0. Since I really need to use FCP for the project for very specific reasons, I made a completely fresh start in another machine using OS 10.9 and FCP 7.0.3. But now, alas, the same problem is back.
Even OS 10.9 might be too new of an OS for full support. Full support for FCP 7 stopped at 10.6.8. Any OS beyond that doesn't take into account the older FCS apps working fully. In fact, at 10.9, COmpressor and Motion break.
You might need to go back further, and possibly on an older system, to have a bug free system that reads timecode properly