The paths have indeed changed from /media_dirs/ID/media_files_data/SIZE/FILENAME to /media/dirs/ID/data/SIZE/FILENAME you should be able to clear your cache table; the same goes for your media_cache files (NOT the uploads).
The /skyline/ prefixed paths should never be used on your site (they are meant to be used by the CMS only and should be password protected).
We have done upgrades in the past and did not encounter these problems. Can you be more specific on what goes wrong?
Regards,
Flurin
Cheers, Luis