As far as I know now :
You can hot rearm/refuel but :
- You have to ditch your external tanks or make the ground crew rearm without and add them again ;
- You can rearm with dumb and laser bombs but you won't be able to change the code ;
- You have to realign completely if you add any GPS guided munitions such as WMCS, JDAMs or JSAWs.
(you'll notice that the INU flag is up on the ADI and that the alignment is 0 on the INS Page)
Note that everytime I tried, the coordinates and altitude were correct on the INS Page. So you just have to confirm the datas with enter and wait.
I usually request ground power and shut the engine down.
I find weird that a re-alignment is needed in this case since the plane knows exactly where it is ...
And off-course the smart munitions are off at this time.
Though I don't know if it is just a DCS behaviour or an actual IRL procedure requirment, maybe something like software or hardware ... or both.
84-Simba's post in Viper Refuel / rearm and INS alignment was marked as the answer