[CLONER] Sub-Site on subdomain multisite network taking "ownership" of primary network

This might not be a Cloner issue, but it's what I was reported as being used when the issue began.

One of my asst designers was cloning our Vanilla store, on a multisite with a few dozen stores. He said the clone produced an error, so he deleted it and created another one.

Unfortunately,

1) he didn't take note of the error (I didn't see anything in the logs)

&

2) he didn't try and re-clone over the erroneous new one. instead, he created another

I've given him the third degree on both items… but that doesn't fix my issue.

The problem is that the most recently created multisite seems to take control over some of the core WP Network files. I've tried removing the site, and then the core files refer to the most recent subsite that exists.

So:

– he created site 28, with issues. so he deleted 28.

– he re-cloned our Vanilla site, which became site 29 (that had no apparent issues within itself)

then:

– i then noticed that the cookies set in async Domain Mapping weren't keeping us logged into our main network site. subsites seem to hold the cookie just fine. (i tried uninstallation, reinstallation, with no resolution)

– i looked through the database, and nothing stuck out at me (but i didn't look through *everything*. only the core MultiSite tables)

– i also tried removing/re-installing a few other plugins, with no luck

– …because, ultimately the problem is that I cannot use Network installed plugins… because it won't save the settings!!! Smush, Hummingbird, etc

oddly enough, clicking on the X on the sign-in box (and not signing in again) makes the box disappear and we're still logged in to the Network site

Fortunately, we're rebuilding another website and are slowly moving over the subsites from Site A to Site B.

So:

– I moved over 29(A) from Site A, to Site B.

– I deleted site 29(A) from Site A

– Now, Site A Network is trying to pull Core files from site 27(A). (everything is fine on Site B)

Now, I realize that this might sounds a bit confusing… so I"m going to post a screenshot of the Chrome error console in my reply.