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
Did you try using the command line way of migrating the data? It is also possible it timed out due to the amount of pireps you have. Make sure the settings in your host allow for that.
You need to go into your host then to phpmyadmin and navigate to the database your phpvms instal is under. Find the navdata table to upload the zip file, if it gives an error, truncate the data already there and then upload the one i sent. This will only work for phpvms v5.5.2/.72 It will not work for a v7 instal