If I own 100% of an interprise can I transfer funds to it at a later time?
As long as neither holding nor enterprise are on the stock market, you can do so at any time via the asset management tool.
Correction to what cookie said: you can not transfer funds, but you can transfer an owned aircraft for free (without compensation) and immediately sell it back at full price, that effectively transfers the cash. BUT you must own some kind of an aircraft.