That should not be a problem, but be prepared that it will take some time until your XP count catches up with the mods count, meaning it will take quite some time until you get the next skill. The XP counter will become higher than the XP threshold e.g. something like 10000/2000 is normal. When the game catches up with the mods XP limit things will turn to normal.
I've… seen things you people wouldn't believe… Attack ships on fire off the shoulder of Orion. I watched c-beams glitter in the dark near the Tannhäuser Gate. All those… moments… will be lost in time, like tears… in… rain.