Fix MissingSetupFile problem without deleting the files

SharePoint health analyzer reports that several setup files are missing on my farm.  The message is as follows:

[MissingSetupFile] File [XXXXXX.aspx] is referenced [3] times in the database [XXXXXXX], but is not installed on the current farm. Please install any feature/solution which contains this file. One or more setup files are referenced in the database [XXXXXXX], but are not installed on the current farm. Please install any feature or solution which contains these files. 

There are several .aspx page layout files and one master page file listed in the offending files.  As far as I know we are still using these files and I am able to locate the files in the _catalogs\masterpage folder.  So what is the problem?  And how do I go about fixing it without deleting the files?