First, with a fresh access token you’re assured that Duplicacy will be granted access to your OneDrive account (since we already know that the token file on your computer expired back in March).
Second, the fresh token will include an equally fresh “refresh_token” that’s required for downloading a new token after 60 minutes (according to Duplicacy’s source code, it connects to https://duplicacy.com/one_refresh to download new tokens).
Third, it helps rule out a problem on the remote storage end. Cloud service providers often use load balancing to distribute users across multiple servers and/or data centers (there’s a practical limit to how big a single server can be).
Unless you’re paying big bucks for service, your data isn’t going to be replicated to every data center Microsoft operates. Microsoft says OneDrive data “[…] is mirrored into at least two different Azure regions, which are at least several hundred miles away from each other, allowing us to mitigate the impact of a natural disaster or loss within a region.” In the United States, Microsoft’s current data centers are Boydton, Cheyenne, Chicago, Des Moines, Quincy, San Antonio, Santa Clara and San Jose.
Microsoft’s load balancer is going to route Duplicacy to a data center that’s holding a copy of your OneDrive account. The choice of data center might be some combination of availability, proximity, network path, system load, etc. When Duplicacy uploads chunk #2, Microsoft’s load balancer is likely going to gravitate toward the same data center chunk #1 was sent to because there’s already a running OneDrive server process ready to receive more data from you rather than routing to a different data center that requires spawning a new server process on an available server node.
Because an access token is a pass into your OneDrive account, a fresh token is effectively a different user (there could be multiple applications accessing your OneDrive account). Microsoft’s load balancer will treat it like any new login and determine which data center is most appropriate. Even if the new login ends up at the same data center, the odds of it also ending up on the same server node are very small (large data centers have huge server farms).
The problem you’ve been having could simply be due to a flaky server, or some kink in a complex chain of connections. Using a fresh token is almost guaranteed to get you onto a different server node and/or data center (which in turn will have a different network path).
(I know nothing about Microsoft’s internal data center operations. The above is just speculation based on personal experience as a system administrator in a data center.)