is this a warning you are getting?
i have never seen that myself, so i guess maybe it isn't?
but then i dont understand your question.
oh, hang on... you mean "Delete Unused Media".
so you have been working with lower res version of your footage, and now want to capture it again at full res.
if that case you are going to be using the "CREATE OFFLINE" mode of the Media Manager.
in this case no media actually gets deleted.
a new sequence with no media in it gets created,
but you DO need to tick "Delete Unused Media"
if you don't, FCP will want to recapture each used clip in it;s entirety.
if you used 5 seconds of a 1Hr shot, FCP will want to recapture the whole 1 Hr.
in create offline mode "Delete Unused Media" will simply delete the unused parts of the shot from the OFFLINE clips,
so FCP will only capture the 5 seconds you have used.
it's a good idea to also add some handles.
hope that helps,
nick