SUPERMAN!!!
Make sure you link your server to gameservers again so there's those statistics and such!
Yes it's possible, on linux, when you in your paintball2 folder (just the base of paintball2, not /maps/ not /pball etc), if you do ./paintball2 +set dedicated 1 +set public 1 +set port 27910 +map airtime - and then if you do another one with port set at 27911 then both servers will point to the same directories as they are based within the same folder.
There won't be any conflict whatsoever.