In your case, don't do a "not", just be less greedy:

$foo =~ s/
           \<\%    # any left doohickey
           .*?     # minimum span of junk
           \%\>    # first right doohickey
         //xg;
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There is a "negative assertion" which really is a NOT, but it's not as useful here as a simple non-greedy match. Read perlre for more information on the .*? non-greedy match, the (?! ) negative lookahead assertion, and the /x modifier for readable patterns.

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