I've seen this only with global vars.Is it just global variables or doe it include local variables?
Do macros saved in 5.49.12, deleted in 5.49.12 and then imported into 5.49.12 generate phantom variables?
No, with 5.49.12 the problem doesnt appear. But since 5.49.13 - yes.
I think, maybe some macros contain some hidden corrupted variables. So MD tries to include that to the Variables page but as unused. I delete it and save mdr, then reload and see them again as MD scans macros and restore that phantom variables. That's my version.
The real problem with updating to 5.53.3 was that in one macro a real implemented variable became substituted to the phantom one. While the macro seemed to be the same. A global variable was used twice in macro - the first time it was performing well but the second time was issuing errors in log with the phantom variable instead, and it caused the macro to be not running well. While it was completely runnable in 5.49.
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