Actually you just need to load some other map between, since q3 refreshes the file list durning every map load. For example:
rcon map test_bigbox; map newmap
ppl wont even notice the test_bigbox loading since it will be loaded/unloaded and replaced with newmap before they get even new gamestate.
The only things that need complete process restart are the options that must be defined on the command line or before any map is loaded.