If that was my assembly, I would do like SWalton says:
1. Get rid of the Flexiblility in all the sub-assemblies.
2. Try to update the top-level assembly and see if the Lightening Bolt disappears.
3. If not, then I would seriously consider getting rid of the ADAPTIVITY and getting those references into those parts another way. I NEVER use Adaptivity, b/c it ALWAYS bits me in the end (so to speak). The bigger my top-level assembly, the WORSE it bites me! And the more work it creates down-line.
4. The parts that 'disappeared' may be way off in 'outer space', so if you select them in the browser and click on ZoomSelected, you may find them WAY FAR AWAY from your assembly, which means you have a Constraints Conflict that needs resolving.
5. If you have Constraints conflicts, then if you turned off Adaptivity, the related parts may be causing it b/c the constraints may be on parts that don't connect due to Adaptivity not allowing the part features to relocate, b/c Adaptivity breaks a LOT, which means the features in those parts may be out of proper position relative to the assembly.
5. In that case, what I would do is find the Constraints that are broken, and suppress them to see which ones will make my assembly go back to normal. You may have to fiddle around with Suppressing and Unsuppressing Constraints to find the offending constraints, b/c many times the healthy Constraints are YellowTriangled and not the broken ones. So it could be a trial-and-error operation.
7. After finding the offending Constraints or part features, then I would work on fixing the CAUSE of the problem at the Part level, which in the case of Adaptivity, may mean a LOT of re-work, or it may mean you can 'cheat' by adding a few work features to the parts in question or 'fake' the dimension by manually measuring it in the top-level assembly and then manually copying that number into the feature of the part in question (all depends on how you modeled your assembly and parts).
That's usually how I resolve such complexities.
Like process of elimination in automotive diagnostics, you narrow it down.
FIND WHAT IT ISN'T, THEN YOU KNOW WHAT IT IS.
... Chris
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