Font color does not change when moving the files to another folder, nor does the color of other files (including PDFs) change to yellow when moving them to the download folder.
If it's in Label Definitions then it'll apply in all folders.
If it's in In Specific Folders then it'll only apply in those folders (or sub-folders, if that's turned on). Anything there should have come from rules defined in Folder Formats in your old Opus 12 config. Let us know if what you have there now doesn't make sense vs what it was in 12, as that might mean there's an issue with the conversion process.
I had a label definition and assignment set up for specific file types (executables) that would make the name underlined orange, regardless of file location. It's no longer there. I recreated it and am back in business.