So I'm in the process of redoing my installation of Oblivion after taking some time off, and going to do full Bain unless it has shaders or obse plugins. And just now I felt like redoing it all together so I selected all my Bain projects and hit uninstall for all of them, unfortunately there seems to be about 15 esps still in my load order...
Was it just overwhelmed with uninstalling some 200 packages at the same time and made some mistakes or is this something that the community is aware of?

If you altered those plugins in any way, via Wrye Bash or whatever, BAIN semi-disowns them. It will not uninstall plugins that are not exactly the versions it installed. Why are you uninstalling BAIN? You could just move it and delete the Data folder yourself, which does not contain any BAIN configuration data.


Edit: I do not know what the references to OBSE and shaders are about, but... Complete Guide to Modified Oblivion - http://tesivpositive.animolious.com/?page=guides_mod_installation&subpage=complete_installation_guide

Sorry wasn't exactly what I meant, I'm reorganizing the way my mods are so that instead of 200+ folders (one for each mod) in the Bash Installers folder there are about 20-30 (one for each group of mods). As such I wanted to Uninstall all my current mods via BAIN, reorganize them, then reinstall them via BAIN in groups.
I was under the impression BAIN didn't handle OBSE plugins or shaders?

Okay. It does not support those file types. You're right.