For some reason, some of the weathers in the .esm reference textures that do not exist. The CK throws a fit trying to package a mod that edits anything in the cloudy weathers because of this. Should I re-link them to existing textures, or just disable them?

And if a dev could read this - the textures being referenced are in the Cloudy weathers, and are:
OblivionCloudCloudyUpper01
OblivionCloudCloudyLower01
WastelandCloudHorizon01
SkyrimClouds02
SkyrimClouds03
SkyrimClouds04
SkyrimClouds06
WastelandCloudHorizon02

Any advice?

What do you mean by "package"?

I played around with editing things:

Unchecking the "Disabled" checkbox, editing the colour of weather types with the textures you mention, but saving the changes doesn't give any errors.

I guess you could just delete the names in the texture box, since those cloud layers are "disabled" anyway (via the new disabled checkbox).

It's not saving the plugin that's the issue, it's actually packaging it for upload to SW or as an archive. For reference, the mod is Realistic Lighting (on the nexus), and in it I've already copied out weathers and edited them a long time back. When trying to package for an upload, it threw an error. After that, I went and checked the Skyrim.esm - and the textures are referenced there. Just straight copies of the weathers aren't able to be packaged and uploaded.

Since they are disabled, I didn't think it'd matter - but I wanted to throw up a questionnaire on it before I did so.