First Answer: I suggest using 'TagLib-Sharp' as ID3 library for .NET
Second Answer: As long as you use a well known ID3 library, your risk to damage the music file is very low. But (as always and with every software) it is not zero. Therefore I would recommend to test your own application with *.mp3 files which you have backuped before.
You could also have the situation, where the ID3 tags have been written to the files not following the specifications from ID3.org. Then the risk to damage the files will be higher. In such rare cases, you have three options:
a) Restore it from backup
b) Rip them again from your original source (CD, LP, Cassette)
c) Download it again from your official market place (Amazon, iTunes etc).
Following the ID3 specifications the ID3v1/ID3v2 Tag is saved in the first bytes before or at the end after the "music data part" of your mp3 files. As long as you delete only this start/end-part, you will not damage your song part.