Fallout 4 mods not activating being deleted by the game itself?

So I've been playing fallout 4 for a while my version is the latest (1.8.*) and I use the F4SE to re-enable mods because most of the mods I use are texture mods and a few game tweaks to make it a little more immersive like one or two radio stations, the chinese rifle from fallout 3 and the wasteland imports. Well I noticed that my place anywhere mod wasn't loading as well as my dialog changing mod that made it more like previous games. So I did some digging and looked in my F4SE plugin folder and noticed placeanywhere.dll and achievement.dll were missing. So I manually added them to the folder and restarted the game and tried to do some stuff in crafting like pick up the trees etc. didn't work so I closed the game and looked back in the folder files were gone deleted from the system. I was wondering if anyone else was experiencing this or if someone had a work around for this. Some mods work fine like true storm and galaxy news radio just a few are having issues

Does F4SE generate a log file? If it does you should check it. I don't know if it would fix your problem, but Mod Organizer keeps your install folder free of any extra files (files other than vanilla). It should be possible to have the game load placeanywhere.dll and achievement.dll through the manager. It stores files in its own folder and it should't delete them should you not be able to find a solution otherwise.

Alright I'll try it, thanks

The Mod Organizer worked for place anywhere and a few other mods thank you.