It’s completely absurd that a council allows either the ALC or the clerk to perpetuate the myth that the clerk determines the agenda.
Check a motion for appropriateness, for spelling, completeness and legality - sure, no problem.
Dictate what does / does not appear on the agenda - err, no thank you and it is for individuals to stand up and oppose this where it appears.
Noting that the premise of the question is that it has already happened in the case where an original motion is so altered as to be unrecognisable, one option might simply be to let it go this time, wait for the meeting then immediately propose an amendment to take it back to what it was originally intended to be.
Not ideal obviously, but it’s an option if you can’t prevent changes being implemented prior to the meeting.