Update: I haven't edited the post below at all, just an update to say I appreciate this is a poor solution and suggest that it isn't used by the poster. My suggestion is way too simplistic for 99% of cases and I'd suggest you read the more learned reply from Davorg above mine :)
If I were you I'd just change your substitution to the generic substitution I've shown here rather than a distinct one for each link...
s#<A HREF="#<A HREF="http://www.mysite.com/#g;<br><br>
Depending on the size of the html file you are producing you can either go over it line by line as you are or just read the whole file into one variable and do one global substitution.
HTH,
Neil
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