Do you actually run single layer tests straight on PEI, or am I missing something?

I keep a glue stick next to the printer for exactly this. I do the same thing you did, print a single layer square to dial in the first layer, but I wipe a thin film of glue stick on the textured sheet first and dampen it with a bit of water. The square pops off with my fingers once it cools and the plate underneath stays clean. On my old Ender I lost a square to the bare textured PEI the same way you did, and that ghost never fully came out either. That was the day I stopped trusting bare PEI for test prints. For real prints I run bare PEI, no glue, because I actually want the grip there. The glue stick is only for calibration stuff where I know I might be slightly too close and squishing plastic into the texture.

On the ghost itself, I had decent luck with dish soap and warm water rather than alcohol. Alcohol alone never touched mine either. A soft scrub with a sponge and some soap got most of it out of the texture on my plate. Worth a try before you decide it is permanent. Also, the fact that it fused that hard probably does mean you were a touch low. On my machine, a well dialed square comes off the bare plate fine when I flex it, so if yours needed floss and a hot bed, I whould nudge the offset up a hair and run another test with the glue layer.

I stopped printing dedicated first layer squares years ago after one welded itself to my old powder-coated sheet and I ended up scraping for an hour. Now I just do the paper adjustment on the Z endstop, run a skirt on the next real print, and tweak the offset live from the menu while it's going. A skirt is only a ring, so if it's squished too flat I can raise it a hair mid-print and the damage is limited to something I'm throwing away anyway. The other thing I noticed on my printer is that a big flat square is actually the worst case for sticking. A single layer square with lots of surface area and no cooling is basically a glue trap. Real prints mostly have smaller first layers per section, and they cool and shrink a little, so they release way easier. My PLA benchmarks pop off the textured sheet with a slight bend of the plate, even when the lines look nicely squished.

For the ghost mark you've got, leave it alone and just print on it. Texture PEI hides small marks and after a few prints you won't see it. Mine has a couple of faint patches like that and adhesion is still even across the plate. If it ever starts grabbing too hard in one spot, a light scuff with a green scrubby pad evens it back out.

The ghost thing is real, but honestly mine faded after a handful of prints. Whatever got jammed in the texture slowly worked itself out and you can't see it anymore. I'd just keep printing on it normally before you panic about it. My trick for test squares is I print them small, like a couple inches across. Little ones pop off way easier than a big slab, even when you're squished a bit low. Guessing yours was a decent size, which is prolly why the floss came out.

Also try heating the spot with a hair dryer before you scrub again, seems to loosen whatever's stuck better than cold cleaning.

One thing I learned the hard way with textured PEI is that the grip is strongly temperture dependent, so if you flex the plate while it is even slightly warm you are fighting the adhesive at close to its best. I now let the whole plate come back to room temp, like genuinely cool to the touch, before I even try bending it, and prints that seemed welded at 40 degrees just release on their own once fully cold. Also, for test squares specifically I print them a touch thicker than my normal first layer, then drop the offset back down for real prints, since a thicker test piece flexes off the plate far more easily than a paper thin one.

I'd push back on the glue stick for calibration idea. Half the point of a test square is seeing how the lines bond to each other and wether you're dragging ridges. Put a film of glue down and you're calibrating against glue, not the plate, and a slightly ugly first layer can hide under it. If the nozzle is genuinely too close I want to see that raw. On my machine a properly dialed single layer releases from bare PEI with a flex every time, and if it doesn't, that's the signal somethig's off, not a reason to add a release layer.