what is the version of mysql you are using? My guess is the server has been updated beyond what your version of phpvms was designed for and thus, you are going to have to look at upgrading to phpvms v7
My suggestion is to do an url redirect to the correct web address, so if it is https redirect t o the https address, so if a pilot puts http and goes that way, it brings them to the correct address
Most likely what happened was the flight number on vatsim did not match thus when acars went to look for it, couldn't find it then assumed it was offline. Also check his vatsim ID is correct.
It doesn't have to be empty, you can have multiple phpvms installs in one db, just make sure they each have different suffix, like one va1_ and va2_ and so forth. But bigger the db the slower the site will be