This seems to be an old issue, apparently ‘solved’ before but still very alive in 9.0.20 (originally reported here, amongst others.
I just found out that the numbering of the VST Instruments changes when you disable or delete VST instrument (tracks). If you have 3 VST instruments, and you delete #1, the system will change #2 into #1 and #3 into #2, in order to keep a consecutive list.
This is not a problem, because the links between midi tracks and VST instruments are also being updated. The problem is this only happens for ENABLED tracks, NOT for disabled tracks. So if VST3 has midi tracks linked and was disabled at the moment I delete VST1, the system changes VST3 into #2, but does not update the links to the VST instrument in the disabled midi tracks. So when enabling them again, the midi tracks linked to VST3 still expect #3, which does not exist at this point.
So I guess the solution would be: every time when the sorting order (numbering) of VST Instruments changes (through disabling or deleting), the system should update NOT only the VST links in ENABLED midi tracks, but also in DISABLED midi tracks.
I’ve made a short video demo, explaining what exactly happens: https://youtu.be/cXfw39TlOF8 Hope this can be fixed asap.