When Skyline sees a folder whose name ends in ".d", Skyline looks inside of the folder to see whether it contains a file named "analysis.baf" or "analysis.tdf". If the folder does not contain a file with either of those names, then Skyline will think that this is an ordinary folder with no mass spectrometry data in it.
What behavior are you experiencing in Skyline? If Skyline is not allowing you to choose the .d folder when you do "File > Import > Results", then I imagine that would be because there is no "analysis.baf" or "analysis.tdf" file in there. Or it Skyline telling you in some other way that this is not mass spec data?
Does your ".d" folder have a file with either of those names in it?
It might be helpful if we could see what files you do have. You can zip up the files that you have and upload them here: