ref 2: files are only deleted from the file system if you press Ctrl-Delete. A simple delete only removes them from MP3tags file list.
On the missing tags:
If you edit data in the tag panel, you have to press Ctrl-S to save the changes.
Also, you should check if you have APE tags in the files (filter for them with
%_tag% HAS APE
And if this is so, then check in File>Options>Tags>Mpeg which tag types your read, write and delete.
E.g. if you read APE but do not save it then you see the empty APE tags but not the ID3 tags.
ref 1.: it is usually not a virus that hinders files from playing but the files are up the spout somehow.
See the FAQs on how to check file integrity: