I am having a similar problem but not in secondary stories line (which I typically don't use). In main timeline:
I have been using FCP since early 7, then used 10.0 which I like a lot (edits sound; renders on the fly, though some aspects are a bit dumbed down).
I recently bought a new, maxed out Macbook Pro, 15 inch Ret., 16 GB 1600 MHz DDR3, 2.8 gHz, which runs Yosemite, so I have to run 10.1.3 or .4.
Great. It's really fast, as I produce, shoot, and edit a lot of video, commercials, and online TV shows. A lot.
Recently I discovered a really disturbing, bizarre thing: clips - generally lower thirds or cutaways on layers above my timeline, are disappearing. I thought I was imagining it, but after a client noticed 1 problem with a file and I corrected it, then she noticed 3 others which were not there before, I know it's a real issue.
It's happening a lot and there seems to be no rhyme or reason - I spent hours, I mean hours, fixing things, then hunting down the next problem. Am considering going back to my old Macbook Pro running 10.0, which runs at a snails pace compared to the new system.
I have tried moving Events and Projects to new Libraries. Haven't tried working as a new Admin yet, but I shouldn't have to.
If there's a problem, I understand, just give me a workaround. This is not predictible and tells me there's an inherent instability going on.
I'm down to importing my exported files and knitting them together just so I get segments I know are ok and which aren't going to change (since they are single mp4's). Ugh!
Help!
Dave