I read I can repair system files with fsck but don't know how.
You read wrong. fsck is for repairing
filesystems, not
system files, and thus will not help you. If you insist on running it anyway, the correct invocation is:
since VPS users aren't (or at least, shouldn't be!) able to access raw partitions.
It won't help, though, since it's extremely unlikely your problem is due to a corrupt filesystem. More likely, the upgraded libraries simply don't work. What you really need to do is determine which libraries are broken and why (error messages are very helpful here). You may be able to fix the issue by downgrading to an older version of the libraries in question. That's all I can suggest without knowing what the problem specifically is.