Indeed, there are several ways for a user to mess this up(trust me, I learned the hard way
). 2 things I will toss out for you:
#1-whenever I import audio, no matter where it comes from, I ALWAYS move/copy it into the session folder, BEFORE I use the Import audio command.(I have had "copy files on import" checked in preferences, but still had imported audio still come up as off-line)
#2-if you open a "template" session and then(once it has opened) you save it to your recording drive, this is not the way to do it. either CREATE a new session from a template(not sure what version of PT you have, so there may be stuff you are not aware of). Or, create a blank session on your recording drive, then go to File>Import session Data>point to your template session and import all the tracks(this was/is the work-around in older versions of PT that did not offer the ability to "Save as Template"(from the FILE menu)