So I noticed with the following configuration where auto-sync is on and update estimates is on, and progress metric is story points where progress tracking for stories is via time spent and remaining estimate, the following loop happens causing estimates in both JIRA P and linked JIRA Issue to decrease even when no work has been logged.
For this example let's say we have an issue that is 10 story points, The total estimated time is 25 hours, 10 of those hours are for a Subtask
1. log work on a subtask under the issue. (lets say 4 hours)
2. Refresh your Portfolio so that progress is updated
3. Plan> Update From Date. – Since work has been done on the issue, the estimate is reduced, (i.e. we are now looking at a remaining estimate) which makes sense. We have worked 4 out of the 25 total hours, i.e.16% and so that would be 1.6 out of the 10 original story points, so we now have a remaining estimate of 8.4 story points. Confirm the update
4. Refresh the Issue, you will see that because the estimates are synced, the story points for that issue says 8.4.
5. Plan >Update From Date-- even though no work has been logged on the issue, it is updating the remaining estimate. I.e. the story points say 8.4, you have completed 16% of work on the original estimate, so reduce 8.4 by 16% and now the remaining estimate is 7.056.
6. Refresh the issue, story point estimate is now 7.056
7. Plan > Update From Date-- even though no work has been logged it sees 7.056 and that 16% of the time based estimate is completed so reduces remaining estimate to 5.92
And so on and so forth.

If no work has been logged since the last update, when I do a plan update it should not adjust/suggest this new estimate. Otherwise I have to remember if there has been progress since the last update and then accept/reject the suggested remaining estimate accordingly.