Thanks @davebYYPCU, Compute All fixed the issue and even preserved things after edits to features.
I'll supply the 3D file anyway. It's in a state where I've got just one mirror support assembly joined to the frame and have not yet created a pattern to clone it.
To reproduce the issue:
1. Find Master Assembly -> Mirror Box -> Mirror Cell -> Mirror Cell Support Assembly
2. Create a pattern using that component and select the Z-axis in the origin in the middle of the Mirror Cell. Quantity 3.
3. Activate the "Mirror Cell" component and verify all the bolts in the support pads are in the right position
4. Manually drag the Timeline marker back to before you created the pattern and then manually move it back to the end of the timeline, or go and edit a feature in any of the sub-components.
5. Observe that some of the bolts are out of position
Again, running "Compute All" seems to permanently fix this so I'll accept that as an answer, but if anyone sees anything wrong with how I've constructed the components and sub components or set up the joints, I'd be grateful for pointers/feedback.
Note that in addition to regular joints, I also tried using Rigid Groups and As Built Joints. They all exhibited the same problems.
Thank you all!