Have you tried moving the parts of your poller microflow that make changes into a Task Queue? So for each update, you make the change in a sub-microflow that you flag as running in the Task Queue. That would move the changes into a new transaction and hopefully allow other parts of your application to also make changes and keep running.
https://docs.mendix.com/refguide/task-queue/#queuing
Good luck!
Maybe create a before shutdown flow where you set a boolean or something that stops the poller flow. Reset the boolean in the after startup. Or use a scheduled event instead of an infinite process for your polling?