To Weird behavior #1:
I have often had the same problem, but not only with “new patches”, but also with changeing/loading already existing patches. This usually happens to me with large patches or patches in which e.g. a “host” module is loaded, which loads a large VST, e.g. Kontakt Player or similar. Very annoying, but I think this has been described here before. A solution would really be very welcome.
It is impossible to save over the template with save, you have to do file>Save template you are presented with an info box asking “Overwrite template patch?”. The only way a .vcv file is overwritten is when it has the same name i.e. “Patch01”. If you want to keep changes in a previous patch - file>Save As and rename i.e. “Patch02”, otherwise it will overwrite the patch as it has the same name.