You are really close.
The problem is that you have a condition, and the coincidence of your rule should be together. Your feedback from the previous one is RewriteCondbroken because it is for REQUEST_URI and not QUERY_STRING as you want.
RewriteCond %{REQUEST_URI} ^/SpecialPage(.*)
RewriteRule ^(.*)$ /$1?%1A%2 [L]
% 1 (.*) URI /SpecialPage. , , . REQUEST_URI RewriteRule:
RewriteCond %{QUERY_STRING} ^(.*)\%(.*)$
RewriteRule ^SpecialPage(.*)$ /SpecialPage$1?%1A%2 [L]
% 1 % 2 , SpecialPage URI .