I figured that there is problem with "umlaut/mutated vowel" in directory names. When latexmk is used and the folder of the tex files contains an umlaut, latexmk doesn't recognize file changes in files apart from the main file. Due to the author of latexmk, this has to do with MiKTeX's way of handling umlauts that are not encoded in a standard way.
I attached a MWE that works correctly if the parent folder doesn't contain an umlaut but doesn't work if it does.
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