You overwrite the default expression. As long as you do it from the convert dialog and not the preferences dialog you don't lose anything, it's only lost for that book. Anyway the default is just an example, it generally needs to be edited in order for anything to match.
file:///.+(\d|(txt|html|htm))
won't get rid of the Amber Lit converter message, that will get rid of headers/footers inserted by browsers when pdf printing html. You'll need a different regex for Amber Lit. Try this:
Code:
(<A name=\d+>\s*</a>)?\s*(<[biu][^>]*>)?\s*Generated\s+by\s+(ABC)?\s+Amber[^<]*(<a\shref=.*?processtext.*?>)?\s*(.*?processtext.*?</a>)?(</[ibu]>)?\s*(<br>\s*)?