Try running an update CHECK now, I pushed a solution that is very similar to something we already had to isolate P3D5-specific profile, because P3D V5 couldn't use profiles made for P3D4 that used custom user-made textures, so we had a optional parameter in the [GENERAL] section of the .INI file that looks like this:
p3d5only = 1
This prevented P3D4 from loading that profile, while still allowing P3D4 to use the version with custom texture names (only possible with P3D4 )
Following the same principle, we now have two new parameters here:
msfs2024only = 1
msfs2020only = 1
To be added to the [GENERAL] section of the profile, like this:
[general]
creator = Fsdreamteam
msfs2024only = 1
This means, the profile will be used only if you are in MSFS 2024 and will be ignored if you are running MSFS 2020.
So, if you have two incompatible profiles for the same airport, edit the MSFS 2024 version to add this line:
msfs2024only = 1
And edit the MSFS 2020 version to add this line:
msfs2020only = 1
I think this is the best solution compared to having two completely separate folders, because that would force you to keep and maintain updated two copies of every profile even when there wasn't any need to, this way you only need to deal those cases where the 2020 version of the airport is not compatible with the 2024 version.