Looks like a bug because unholy blessing doesn't remove any progs from all other weapons, only flags.

No problems here.

Can you explain why that is intended to work that way? Ghostly scimitar has been used over the years as a common light sword, particularly for the proc getting through defenses, and not removing progs is one of the key reason certain items are picked (screaming mace, duergar king axe, thunderlance, the old ST weapons, etc).

Because it was made to work that way - simple as that.

You can still use ghostly scimitar as a light sword and to get through defenses.

Not every weapon is as friendly to unholy blessing