This seems to do the trick:

s/(\\*)(#[^#\\]*)/length($1)?length($1)%2?"$1$2":$1:""/eg;
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And hear it is again, in a more readable form:

s/(\\*)(#[^#\\]*)/

## Matching anything before a pound sign, putting (back)slashes (or la
+ck thereof) into $1. 
## Also make sure that we do not grab any slashes and pounds after the
+ first pound
{
if (length($1)) { ## If we found some backslashes
  if (length($1)%2) ## If there are an odd number of backslashes
    print "$1$2"; ## Return all slashes and pound - this is not a true
+ comment
  }
  else { print $1; } ## Even number - return only the slashes
}
else { print ""; } ## Return nothing, this is a comment
}
/eg;
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