I can't speak for Rotax however in most engine overhaul shops they install a new filter after the engine has been test-run as the filter check is part of the post-test inspections that are carried out prior to shipping the engine out the door.
As you suggested, for a start remove the filter and see whether it looks new or used. If its new you're away laughing. If its definitely used I would probably be inclined to use it for the first few hours and then replace it.