I can't reproduce this in TP10.. when I right-click on a greyed-out folder I still get the "Remove Orphans <Ctrl+Del>" option there.
A greyed-out folder no longer exists on the hard drive, but TP still has thumbnail records in its database for files that used to reside there. You must have "Options | Preferences | Thumbnails | Show Orphans" on to see them (recommended).
If a right-click on the folder doesn't bring up the required command, I think TP5 still offers 4 other ways of getting rid of orphans:
1) Use "Thumbnail | Remove | Orphans" from the menu (or its TP5 equivalent)
2) Turn on "Options | Preferences | Thumbnails | Auto Remove Orphans" (or its TP5 equivalent), then browse those folders and their orphaned records should disappear, along with the greyed-out folders themselves (a Ctrl+F5 refresh of the tree may be necessary).
3) Go to the top-level folder, and use the Remove Orphans command from there, specifying 'Current Tree' so that subfolders will be cleaned of orphans too. Note that this may also remove orphans from other subfolders that maybe you'd wanted to keep.
4) Delete them manually by selecting them and pressing Shift-Del.