The flats scenario you have shown in the original post, is what I called the “embossed mote” or the “white mote” these occur when the flat corrects for a defect that is no longer present. This is different than a “dark mote” or “black mote” as I call them, these are defects that were present, that the flat did not correct for at all.
The only way to solve the black mote, is to have flats with the same mote in them. The only way to solve the white mote, is to use flats that did NOT have the mote in the flat, that was not present in the lights.
This is why we take flats every single night, and we use automation software (Minerva) to calibrate data daily with the fresh flats taken. Even with this level of consideration for flats, we still run into situations where the mote moves once or more over the course of the night, and ruins the lights.
In this case, you have a few options.
Hope the one or two frames with uncorrectable white or dark motes, are buried in the pixel stack and not visible. This is actually easier than one would think it is.
Obtain a set of flats to correct either case properly.
Use clone stamp to remove the offending motes. Or use PS for similar means.
Reshoot the lights, and throw away the bad ones.
Motes are a pain at times, and is a good reason to keep the camera, filters, and window clean as best you can do. Using a nightly regimen of sky flats can really reduce this issue very close to zero.