Dear Mike,
What a fascinatingly horrifying story!
The "best" thing to do IMHO is to remove all, or most, of the varnish all over and then redo it. This will ensure uniformity again. That is, assuming no paint will be removed with the varnish. However, before going that far, why not just try to remove a little bit around the area of the current "hole" in the varnish--just enough to get rid of the ridges. Then, mix up your best guess of the matte/gloss ratio and patch it up. If, after drying, it looks noticeable, then you're simply back to having to remove all of the varnish. If not, then you're good-to-go. What do you think?
To remove the varnish (in case you haven't had to do this ever before) start by using the mildest solvent and work up from there. You want to use the mildest solvent that will get the job done. For instance, methyl hydrate will certainly work, or toluene, but these will also remove the paint very easily. But, perhaps naptha or some mild mineral spirits will work just as well, and still spare the paint layers.
If the paint was well-cured before the varnish was applied to it, then it should be pretty well able to withstand all sorts of solvents. I've successfully removed varnish using odorless mineral spirits (Gamblin's) and those blue shop towels you can get at any hardware store. They are strong, absorbent and, best of all, lint-free. I prefer them to cotton swabs. A restorer semi-acquaintence once "helped" me by removing some damaged varnish from a painting for me using a cotton swab dipped in the solvent. It removed the varnish all right but it left behind a zillion little cotton fibres which I then had to remove, one-by-freakin'-one, with tweezers! Arrgh.
By the way, are the Liquitex varnishes Hard (High Molecular Weight) or Soft (Low Molecular Weight)? If they are the former, then they will not settle, or level-out, as water does. Rather, they will conform to the contours of the surface they're applied to, so that is why you'll want to ensure those ridges are gone. With a soft varnish, the ridge wouldn't disappear, but it would be less evident.
Good luck.
Juan
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