Yup, annoying like hell, I added 1 mod currently to the pack, so each time I do an update, I'm forced to never forget to put it back in the mods folder, if for any reason I forget to do it and start my server, my world will loose a lot of stuff from Binnie Mod (Extra Trees/Bees)...
I also have to remember my players (currently only my brother and cousin at the moment) to put back the mod in their mods folder, same thing goes for less critical mods like IngameInfo, ArmorStatusHud and StatusEffectHud, I have to put them back each time, for me, its not a real problem since I use MultiMC5 and can control what I add there easy, but for my cousin and brother that are stuck with the FTB Launcher (they don't want to hear anything about a better option at the moment both had a lot of troubles in the past with MultiMC while I never had any issue with it)