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So the skip token I get from graph API is a number, based on my understanding(I might be wrong), it indicates how many emails need to be skipped.

In our application, we store that skip token in our db/memory so we can fetch next page of emails. So if say a users current skip token is 100, and before we send a request to the server with skip token 100, that user delete 10 emails, then what gonna happen if still use that 100 skip token?

Since I am not sure how to deal with this kind of user delete emails case, the way our application works is: we always do a minus on the skip token(like -10), and check if we can find any email or timestamp overlap between current response and previous response, if there is no overlap, we do another minus to the skip token. It is kind of like walk backward. We stop doing minus till we can find an overlap.

Does it make sense? So far, I noticed some skip tokens's responses give nextLink as null while there are still new emails in user's inbox. Also, we missed a couple of emails for around half year(meaning that the email is in user's inbox but not fetched by our application).

The Delta Query (Track Changes) API might be better suited for your needs. It effectively allows you to keep a "bookmark" in a change log of someones inbox.

E.g. Instead of keeping the skip token you would keep the deltaLink you get back from calling /messages/delta. When you call the API again with the deltaLink you will get a set of changes back since the last time you called the API + a new deltaLink. This allows you to keep "in sync" with the changes going on in the inbox you are monitoring.

The API reference docs are here:
https://docs.microsoft.com/en-us/graph/delta-query-overview