Zach,
I'm happy to check out a file if you can share it.
As far as OpenVSP is concerned, Advanced Links only depend on the values of the input Parms. If an input Parm value does not change, then the link will not be recalculated.
If your gear is attached to the wing -- and the location it is attached to depends on dihedral (for example) -- but dihedral is not an input parameter to the Link, then VSP will not know to update the link when dihedral changes.
I can think of a couple of workarounds for this...
1) Make dihedral an input variable to the Advanced Link -- even if you don't use it in your calculation, it should make your link 'sensitive' to dihedral.
2) Add a Probe to the wing at the location you're interested in matching. The Probe will calculate output Parms that you should be able to use in the Advanced Link as inputs. Those should update whenever the surface moves or changes -- no matter the root cause.
Or it might be a bug...
Rob