You should really, really stop doing uninstalls and reinstalls. There are only a few situations where that fixes an issue that couldn't have been fixed inside MC. I don't think your issue qualifies, from what I know so far.
You also should not be directly copying and moving files in MC program directories to try to reinstate default media player settings, unless you really know what you are doing. There is no file you can delete to reset settings to default. All settings are stored in the Windows Registry.
If you really, really need to get back to the default settings, this is one of the things that does require making a Library Backup, a full uninstall, including the Library and all settings, and then a reinstall without letting MC find the old Library. The default settings would then be visible inside MC. If you then want your Library and Playlists back, Restore the Library Backup you just made without settings. However, while that will give you the default media player settings, you will need to set everything up again from scratch, for your local hardware, preferences, etc. That could be a lot of work, depending on how complex your setup was previously.
So if you have lost some player settings, Restore an earlier MC Library Backup. MC makes regular Library Backups, so there will be several to choose from. If that isn't viable, just fix the settings inside MC. It isn't hard. I assume that you did Restore a MC Library Backup after the un/reinstalls, or that MC found the previous Library and used that, so you should have what you had before. If it doesn't work, fix it. If you don't know how, explain your setup and the issue you are having, and ask for help on that issue.
On the issue of making "the missing file links within Media Center just disappear", if you have the Auto Import setting "Fix broken links" set to "Yes (protect files on missing drives)", and you run Auto Import or it runs automatically, then the missing files will be removed from the MC Library. That works. If it hasn't happened, it is because you don't have Auto Import set to run, and you haven't run it manually, or you have your media on an external drive such as a NAS or a USB drive. If you do have your media files on an external drive, set "Fix broken links" set to "Yes" and run Auto Import.
Go to the top menu > Tools > Import > select "Run Auto-Import Now", and click Finish to run Auto Import.
Check if the missing files have been removed. If they haven't, come back and report here.
If the missing files were removed, then go to "Options > General > Library & Folders > Auto-import > Run auto-import in background" and tick the box.