A simple text file that contains a list of deprecated stuff that gets read by DR and can be used to mark the specific assets in question, for example by using a different text color (brown or red for example). In regards to replacing stuff "at some point" I guess it is enough to check whether missions have been updated and if in that case some of the assets in question are not used anymore. This would however only be worthwhile once the list of deprecated assets reaches a length were removing them from the mod would make a noticeable difference in file size, which probably mainly counts for image files anyways, as most other stuff is not that big.
The most important part for now should be to create a list of assets that needs replacement, at least to get an idea of how much we are talking about. Secondly feedback from anyone working on the coding side of DR in regards to possible implementations is needed, otherwise we don't need to discuss this aspect any further. Once we have these things sorted we can specify the details.
Just my oo