Your best bet is to revert the built-in content to original, then follow the second set of instructions to fix the 'false faults'.
To do this (if you are not sure):
1.Go into Content Manager.
2.In the search pane, use the following search:
LOCATION=LOCAL
BUILTIN=TRUE
FAULTY=TRUE (you may not need this one)
3.When the results appear, select them all (Ctrl+A is a useful shortcut here)
4.Right-click the list, then select Edit.
5.Click 'Revert to Original' if it is available.
For non-built in assets (and built-in ones that do not show Revert to Original).
Follow instructions 1 to 3 above, but you do not need to include Builtin=True in the search on step 2.
4.Right-click the list, then click View Errors and Warnings.
5.Once this is done, click Close - any assets that are not actually faulty should disappear from the list (the ones that remain have genuine faults that would involve either downloading the updated version using View Asset Versions>View in Main List or fixing the items.
In terms of the missing items, look for a quarantine feature in your security software - they should appear in there.
Hopefully, this will either sort out the problem, or make it simpler to deal with.
Shane