You know what, I'll give you a hint...
What is your merged plugin's name?
ClocksofCyrodiil+ImprovedSigns(complete)+ImprovedSoulgems Merged Plugin.esp
I wasn't very creative there.
Unless there is an esp with a corresponding name or you add the BSA to your ini file this is to be expected. You need to merge all the meshes and textures from your merges mods as well, and then build a new BSA with the same name as the merged ESP.
Do you mean bsa?
Improved Soulgems seems to be the only mod affected that I have noticed. All clocks I have seen in Chorrol, IC, and AU are visible. I already extracted the bsa and ran pfyyi on it while I was at it. I just wasn't sure what to do next.
You could also just unpack the Improved Soul Gems BSA.
I thought about doing this as well with just remaking the archive but limited knowledge past all this. I would prefer to keep it as-is.
Let me get this straight. I should now repack uncompressed into a bsa with the above name and that is all?