I just made the reproccer.esp, and then i saw in Wrye Smash that the box next to it is orange...

http://i176.photobucket.com/albums/w172/Illius_photos/TES/Problems/ReproccerBoxcolour_zpsed447592.jpg

I assume it is because the Unofficial patches are placed by BOSS where Wrye Smash does not expect them to be. Will it cause problems if i keep the reproccer.esp like that, or do i need to do something else?

Reproccer is a dynamic plugin, right? If you rebuild it, everything will definitely be fine. Everything will be fine anyway though, in this particular case.

I think so, it is an automated patch generator for SkyRe.

http://www.nexusmods.com/skyrim/mods/28467/?

But if you believe that this with the reproccer.esp is fine then i will start playing, thanks Wrinklyninja.

Has that ever been updated to account for false flagged ESP files acting as master files? Like the ones for the unofficial patches and/or Wyrmstooth?

By the look of it. the Reproccer download was last update the tenth of October 2013, but i do not know when when the Unofficial Patches where made into false flagged ESP files acting as master files, so it is very much possible that T3NDO has not made changes for that with Reproccer. I just send him a PM on the Nexus, asking if he could take a look at this thread.

The USKP change was in early beta by Oct 10, public release wasn't until November though.

I see...well now it is just waiting to see of T3nd0 can shed some more light on this.

Alright after having PM'ed a few times with one another this is what T3nd0 mentioned.

So that confirms what you already mentioned Wrinklybibja.