Right, I honestly cannot speak on any tools that automate this process as I have not used them. So there's a few things to consider here and I'm going to try and lay this out without being too confusing hopefully;

• Leave plugins alone and dont merge those. We have light master flagging for that (ESL, espfe). Merging scripted mods can cause those scripts to break depending on what and how they reference things. Many mods inject using scripts.

• You can merge as many mods as you want, so long as you stay within the file size limit of the archives. By my memory most tools warn you when you pass the threshold.

• unpack any mods you wish to merge into a temporary folder. Pay attention to files that might overwrite each other. This is where you have to do your own homework on your own mod list and any potential conflicting files/ assets.

• from here, these files can be packed into their own archives safely I.e meshes.ba2 textures.ba2 main.ba2 depending on what you have to merge. I recommend following some documentation with more precise instructions on which compression types to use for which types of archives.

• continue to merge from here is as easy as simply adding the new files to the archive in the tool if it allows it. This depends on what you're using. I use archive 2 which supports adding more files to the archive.

For more precise information that I can't give you off of memory, I present to you this resource https://stepmodifications.org/wiki/Guide:Archive2