Yes, unless it's part of the operating system install, it will be deleted. Be sure to download drivers before starting the install just in case you can't get an internet connection with the computer after the install. An even better idea would be to use another computer that hasn't been compromised and have it ready with an internet connection once you're installing.
Something to note is that a vendor you use may have been compromised by either a hack or an employee. If you haven't seen your bank account emptied, I think this vendor problem is more likely than someone hacked your PW manager.
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