The rate limit error comes from Canvas. An API Rate Limiting article in the Canvas Community notes,
"Canvas monitors API requests to prevent abuse and/or excessive use. We do this to ensure that the rest of the environment and other schools are not negatively impacted by a single user or application. Canvas limits are imposed at the token level, so it’s helpful to create a separate token for each application that has a significantly different purpose."

Here are a few things that you can try to mitigate the issue:
  1. Try varying the way you update. If you have been changing all of the assignments and then selecting update after all of the changes have been made, try updating with smaller groups to space the requests out more.
  2. Try deleting the authorization from your user settings, then relaunch the tool to see if a new token resets the limits.
  3. Have another user help with the process so the requests are split between multiple users.
This is a continually moving limit, so taking a break for a few minutes between courses or groups of assignments might help prevent hitting that mark.