Redirect domain/folder%10two/index.php to domain/folderthree/index.php :
RewriteCond %{THE_REQUEST} ^[A-Z]+\ /folder\%10two/(index\.php)?\ HTTP/
RewriteRule ^. http://example.com/folderthree/ [R=301,L]
Note that you could avoid having to use one rule for each URL if you kept the same "number" in the new URL. That is, redirect folder%10two to foldertwo and folder%10three to folderthree instead of changing the number.
In that case, only one rule would be required for all "folders." For example :
RewriteCond %{THE_REQUEST} ^[A-Z]+\ /folder\%10([a-z]+)/(index\.php)?\ HTTP/
RewriteRule ^. http://example.com/folder%1/ [R=301,L]
-or-
RewriteCond %{THE_REQUEST} ^[A-Z]+\ /folder\%10([^/]+)/(index\.php)?\ HTTP/
RewriteRule ^. http://example.com/folder%1/ [R=301,L]
Also note that I did not include the "index.php" URL-path in the new URL, and that I made it optional in the RewriteCond pattern. We generally recommend against 'exposing' your site's technology either by redirecting to /index.<filetype> or by linking to it, because the technology/filetype might change, requiring you to change all of your URLs again -- something to be avoided if you care about search ranking and user experience on your site.
Instead, link and redirect only to "/" and use DirectoryIndex to map "/" in any directory to /index.php in that same directory (if this is not already done in the existing server config) using
DirectoryIndex index.php
Jim