please list everything that you changed between the study that worked and the one that didn't
first guess is that your files aren't local. make sure they aren't in a dropbox or anything like that. test with the files on the desktop.
second guess is that you've got a lot of local bonds..etc these take time to compile at the start of the analysis, hence the question about what exactly you changed.
third, install issue. do other analyses work ok? if so, the software is working ok. if others aren't, you might have an install issue and rather than it being a change in your study, it may be a change in your computer that is causing the issue. your comment about cwmesh erroring, makes me think this may be the case.
could there be a software bug here? possible, i'd have your reseller take a look at the model.
database not found can be caused by lots of things. for example in nonlinear it can be because you ran it once and it is showing a time step that doesn't exist in your new sim. same goes for transient thermal. create a new plot to check this. we also had a customer recently disable calculating stress, so when they tried to plot stress, database not found. it can also happen if your file is disconnected from the results. this can be because of things like dropbox or not using PDM properly. i'd suggest starting a new thread about this and talk about your workflow and if it happens on other models.
on your last question, i'd start a new thread. that sounds like a soldiworks issue. i'm not sure what you mean by layer color.