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When looking at the server locally, the servers said that they had 40 patches applied during the same time frame.
This part is confusing. Were you looking at Windows Update for this?
Did you deploy patches from Protect at all? The only way it's going to go from showing 20/26 missing patches to showing none missing is if patches are applied. I'm guessing if deployment was never run from Protect that Windows Update or something else was run on the machines and applied updates.
Maybe some screenshots would help clarify what you're asking?
We were not looking at Windows Update, were looking in the Programs and Features / Installed Updates Section. Then looked at the timestamp of all the installed updates.
For these servers, the only way we deploy patches is from Protect Standard.
I will try a screenshot, but the patches we have applied were backed out manually, because it broke the app.