It seems if a protected logical file is added to an empty super file, the superfile inherits the logical file's protected status, with the knock on effect of then being unable to remove the subfile and having no way to unprotect the superfile inside Eclwatch. The only way to unprotect it is via daliadmin unprotect.
1) I don't think the superfile should be automatically protected in this way
2) It probably makes sense to be able to protect a superfile (and you can already via daliadmin). Eclwatch should allow it also.