Call a function in the substitution part (activated by /e modifier) which returns your transformation.

s/PATTERN/replace($1,$2)/eg

Not sure if you even need to pass the matchgroups $1,... into the sub, but it's certainly more readable.

Edit

Pattern should match the links [$1]($2) (pseudo syntax).

I recommend using the /x flag for readability.

The transformations of $2 should happen inside the replace() sub

HTH!