Either you have 200GB or 50GB, you cannot have 250GB icloud storage.
You also cannot look at the GB count to setermine if photos or data are missing. Apple software will compress or expand photos as required.
The number of images being 9000 not 11000 is your problem and there is no way of knowing how you lost them.
It has never happened to me either using Mac-phone-Mac sync or more recently iCloud Photos.
Somehow you deleted them or ran out of storage. A possible way is to have too little storage or letting the rental skip due to credit card problems more than 1 month. Or having 56GB of photos on a 50GB storage plan.
Getting them back after more than 30 days will be impossible if that is the case.
Ask Apple Support
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