You can copy your character over multiple times. As long as you have a free character slot on Tribble. (Holodeck characters slots != slots in Tribble) Don't delet the character you are using to test out the new stuff. But remove an old character if you need to.
Maybe I've just lost the plot or I can't understand this multi-layered currency system, but surely being generous with the Omega Marks but stingy with the BNPs is counterproductive? If you have more than enough Marks but need BNPs to finish a project/buy something, why bother having the Marks when you'll need to run the same missions that give them anyway?