I saw this recent post about someone's RE score changing because they updated their heart rate zones. I have a similar problem, but I did not change my HR values. Instead, I added a Pace Zone based on a recent 10k race result.

You can see in the individual activities which ones were before I added this zone because the Pace Zone area at the bottom asks you to update your profile to get a pace analysis. My first run with these zones populated is on March 14. Since then, despite going through the peak of my marathon training cycle, my 'fitness' has gone down based on Strava's RE calculations.

The trend line change is directly tied to how that RE score is calculating since I added those pace zones. This is pretty clearly seen in two runs on a similar route.

First Run  - March 9th, 16 miles, average pace of 9:27, average HR of 168 BPM, RE of 407. Notice that the zones are not populated at the bottom.

Second Run - April 13, 20 miles, average page of 9:29, average HR of 167, RE of 274, pace zones are populated here

You can also see in these screenshots that the HR zones did not change!

These two workouts are not the same, but the second was longer, more elevation gain, and a similar pace and still has an RE score of 130 points less.

This drastic difference can even be seen in much shorter workouts. I run every Tuesday morning with one group, pretty steady and easy, roughly 6 miles.
Group Run 1 - March 5, 6.2 miles, 9:35 pace, 159 avg HR, RE 112
Group Run 2 - March 19, 6.49 miles, 9:46 pace, 153 avg HR, RE 39

Is there any way to fix this? I'd rather get rid of the Pace Zones entirely if they're throwing things off this badly. But it's pretty frustrating to see that when I paid for Strava and added pace zones it started to completely mess up this calculation!