Sometimes one really needs to create dynamic queries, and then there you go : Partial (or even complete) Queries migrate from advanced query widgets to assigns...Urray professional bug finders : take your challenge.
I throw to the thin, odd summer air, two possible solutions for this :
1 - Live with what you have and build above it solution
Check inside assigns (either all assigns, or recursive checks into advanced query input parameters assigns) for query parts, just like you were validating advanced queries....
2 - Apply the build to change, and add a new feature to Service Studio
As you have special keyletters/words detected inside Advanced query, there could be some kind of letters that would indicate : Beginning of condion , End of condition; Begin of conditional code, end of conditional code.
Something Like this
Inputs : @Condition1
Select a.* from a
inner join b on b.Id = a.bId