Have you heard the expression "Going to the well once too often?"
You should start new threads when totally new questions arise, so that others can find them with a search and learn from them. This has nothing to do with the original question and title of the thread.
First of all, stop renaming files outside of JRiver and causing yourself problems. Use JRiver's "Rename, Move, and Copy Files" dialog to do it, and nothing will break. The function is very powerful, and since it can act based on metadata, should be able to do almost anything you need.
Learn about it here:
https://wiki.jriver.com/index.php/Rename,_Move,_and_Copy_FilesThose red do-not-enter signs (dots) indicate you have broken the link to the file, by messing around at the file system level without JRiver's knowledge. You've changed the file name, or moved it or deleted it, but the MC database has not been updated.
To find all of the broken links, create a new smartlist named "Broken Links".
In the Edit Smartlist dialog, have one rule of type Custom, and paste the following text as the rule:
[=ismissing([filename])]=1then click OK to add the Smartlist.
When you browse that smartlist, it will show you all the broken links. You can delete those files from the library, and then reimport them from wherever you moved them to, or you can use the rename/move/copy dialog to fix the paths.
If you insist on messing about at the filesystem level, and don't like MC consequently removing broken things from the library without your knowledge, you have two options:
1. Uncheck "Run auto-import in background" and don't manually invoke auto import either.
2. In Configure Auto-import, set "Fix Broken Links" to NO.
In either case, references you break by altering the file system will remain in the library, and you can find them and fix them with the smartlist.