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I think it depends on the mod and the update. The last update did not change the files I modded "Simconstants, battleconstants and contract folder" but the first one did. Make a copy of your modded files, then you can bring them back in after the update.
 
I checked after the last update, seem like the majority of my tweeks were unchanged. This game is great but when you just add TH mods for range, reduce lrm stablization damage, and add a 1 cheveron for any movement, then tweek the weapons just a touch, its amazing. ( PPC -5 heat, +5 damage, LRGL -5 heat +5 damage, ML +5 heat) Love the game!