I'm going to be very careful here, not only because I've been a faithful Cakewalk user for decades, but also because I admit that I haven't been methodical about documenting these things, but I have experienced these same issues. Specifically, loading project with frozen tracks to discover than I can no longer unfreeze them, or that MIDI no longer seems connected to the instrument on that track. I've had to recreate tracks numerous times because they become "broken" in some way. I've not reported it because by the time the project gets to this point, I don't really have a good recipe for how it got that way. As the OP states, once a track exhibits a problem, it seems to ripple around causing more problems to pop up. I'm well aware that this is not a good description for tracking down actual bugs, but it is real.
FWIW, I started to think it was related to freezing/unfreezing. I would occasionally freeze an instrument track and then edit or apply FX/gain curves to the audio track. I think it may be that these tracks were more likely to start having problems, though that's not in any way a scientific observation. So I stopped using freeze and instead, now bounce to track and then archive and hide the instrument track. I want to say this has improved my experience but I'm not sure I've had a sizeable project since I started this.
I'm only piping in here because I want to lend some credence to the OP's frustration. I've felt it as well.
I recently reinstalled everything on a new computer, including all of my plugins. When I open an existing project, Cakewalk complains about several missing plugins (Omnisphere 2, for example), despite the fact that they have been successfully scanned, are in the installed list and can be used in new projects. The only difference between the two installations is that the plugins are on a different drive - same path but with a different drive letter. Research on this forum implies that plugin absolute paths are not saved in a project file and shouldn't matter, but my experience seems to contradict that claim. I haven't found a solution to this, and unfortunately, I don't know how to re-insert the missing plugin on an existing instrument track in a way that retains all of the original plugin settings. Anyone have any experience to share?