Odds with ZTL appeal

Appeals to the Prefect are free because they are meant for such cases, where there has been a clear mistake and you ask the cops' monitoring body to correct it. I would attach also a copy of the return e-ticket.

Are you 101% sure that November 17 is the date of the violation and not the date cops were told your name&address? Who sent this notice and how? If this is a registered letter from Multiservizi, the rental car company should have charged your credit card some weeks after you dropped the car off.

I'm not 100% sure but the notice I received (today, April 29 2019) only has two dates on it. The form was in English and said "Date of the violation 17/11/2017" and "shipped on 18/07/2018" I would assume the shipped on date means something like the date they requested the information from the rental car company or got it from them but I'm not sure. (I wasn't in the EU on July 18 2018 either.)

I was in Bologna in Sept 2017 and it is possible that they got the date of the offense wrong, but I how can I establish that they meant a date other than what they listed. (I did enter the Bologna ZTL in Sept 2017 to drop off bags at our hotel, which is permitted. I have the booking information for the hotel that matches the actual date I entered the ZTL but it won't match the date of the violation in the letter, since I wasn't in Italy.)

I have read horror stories that appealing to the Prefetto office is basically a waste of time and can cause your fine to be doubled if they determine your appeal to be baseless. I would like to think that my argument (I haven't been in Italy since Sept 2017) would hold merit, but if I'm risking having my fine doubled against a slim chance of a fair hearing, I'll just pay the fine and avoid Italy for future trips.

“i’ll avoid Italy on future trips.”

Nonsense . Go to Italy but pay attention to the ZTL signs. They are highly visible.

I would leave out any mention of entering the ZTL to drop bags. You only have to establish that you were not in Italy on the date of the alleged ZTL violation so it could not possibly have been you.

Listen less to silly horror stories, If you are not 100% sure that you are right you don't appeal for free to a Prefect but to a Judge. The Prefect corrects clerical errors like a cop writing down the wrong plate number.
It's the dates that don't match with the law. Was your credit card charged by the car rental company? When? According to the letter from Multiservizi, can you pay with a 30% discount within five days? If not this is a second notice.

I'm sure you warned your hotel you were going to enter the ZTL in September, asked your plate number to be put into the white list and followed the shortest route from the ZTL border.
Since You have no reason to speak about unfair hearings, you have no idea how the system works and base your opinions on "stories"... I'm afraid we won't miss you that much, just a little.

If you were not in Italy on the date of the violation, then you absolutely should appeal. You need only show your return ticket date and that should be enough.

I'd also take it up with your rental company, if you still have the paperwork. They would have charged you an administrative fee, which appears to have been in error. You should get a refund for that.

Assuming you are reading the letter correctly that is clearly a mistake they made.
You don’t have to worry because nothing will happen to you if you don’t pay. Just write to them, explain your situation, and wait for an answer. Write in English with a Google translation attached.
If tomorrow a collection agency asks for the money, send your documentation you sent to the prefect or peace judge, and if they insist to be paid (as they might since they try even when they are wrong) just threat court action on them.
If they report you to Equifax, have the report removed based on the same grounds.
75% of fines incurred by foreign drivers never get collected even when they actually committed the infraction and absolutely nothing happens because those fines are not enforceable in foreign courts.