Well that could be done with another program running alongside FL, although the problem would be when the files are loaded, are they loaded once at the beginning or everytime you launch

Which jumpholes/gates are locked is saved in your .fl file, so any changes made to the server-wide locked/unlocked would only affect new characters made in that time period. Now, if you combine this idea with other ideas that have come this way about similar things, such as factions and such, you could concievably have a player who's affiliated with the rheinland military, and for whom the jumpgates through the sigma systems are locked (because the GMG controls them) and who would have to use the jumpholes. at the same time (but obviously, created at a different time), you could have a player affiliated with the liberty rogues, for whom all liberty jumpgates are locked, or perhaps even all lawful ones. Of course, this might be easier done if one can simply find a way for hostile jumpgates to deny entry.