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I recently adjusted my HR zones on Strava based on the fact that 

A: I'm getting older and my max HR is probably lower than when I signed up for an account

B: My PRs are slower, as I've suffered from injuries

C: My RPE at various HR.  For instance, I feel like I'm at LT1 (aka the top of zone 2) at about a HR of 130ish.  The auto settings had this HR set at 139 previously, so I lowered it to 130

All of these things should mean that Strava recognizes that I'm in a higher training zone at a given HR.  However, after making the changes, my relative effort numbers have been very low, compared to where they were for similar runs or rides.  

For example: 

Today's ride, power output of 109 watts for 1:20 ish.  RE of 17

Similar ride from last week. 113 watts for 1:20 ish. RE of 80

Looking at the heart rate zones for both activities you didn't change much, the top of zone 2 was 141 on 24th of July and 139 yesterday. And the newer activity has much lower heart rates therefore it's consistent to get a much lower relative effort. The estimated power output is not relevant, the relative effort is based on heart rate only.

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