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It could be fleas, allergies or it could even be a bigger problem.
Because she is not eating well, you need to see the vet on Monday. She might have a treatable condition today that won't be if you leave it much longer.
Let me know if you have more questions.
<<In fact, it turns out that this is an autoimmune disease that all cats get throughout their lives. >>
This is not true...and question where this information came from. "Autoimmune diseases" are not common and do constitute a "bigger problem" as Tammy suggested. The lesions you described can be from everything she stated as well as an immune mediated issue...but for that to be diagnosed a biopsy of the skin needs to be done...which I assume wasn't done.
I feel like you received a good answer from Tammy...and your vet failed to explain the issue with you very well.