[Baron Grazic]

Hi StarJack.
Resupply is instant, but it does not give you instant full supplies. The Resupply Facility only gives you a certain amount of supplies. Check the Resupply Facility for details.
You said you were retro-fitting your ships? If your new ships have newer engines, then most (all?) of your supplies vanish with the old engines.
I learned this the hard way. If you retro-fit your engines, move the supplies to the planet first...

PS. Cheat code for resupply = ~restoresupplies~