In addition to the problem leriksen pointed out, your suggestion deletes an extra character. In order to meet the OP's spec, it gets a bit uglier:

  $str =~ s/^%q|([^%])%q/$1/g;
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Basically, it would be less confusing to learn about zero-width assertions.

Granted, it does pose a bit of a challenge to "learn" the various zero-width and non-grouping forms. I haven't memorized them yet myself -- I just scan through the "perlre" man page every time I need to use one of those "(?whatever)" thingies. I actually don't mind that. I'm used to it from always having to do the same thing for a dozen different common C library calls -- I still do that, after "knowing" C for 15 years.