I found this article on relative effort https://support.strava.com/hc/en-us/articles/360000197364-Relative-Effort which references perceieved exertion as well, I think if you adjust that for the 2 activities it should rebalance it. Would be good to understand the discrepancy as I'm not sure what the difference in HR zones were as they look pretty close in the screenshots.

Hello Vik,
Thank you for your reply. I have already checked this. But in both activities the perceived exertion is off, so this can't be the problem.
You see no differences in heartrate zone because I changed my settings back.
The HZ zones were a little bit higher when I uploaded the 17km activity (Z5 started at 179). 

Hi @JasperH 

Thanks for your post. As @VikK mentioned, setting a perceived exertion on one of the activities would be one way to adjust the relative effort so it is more in line with what you were expecting.

The reason for the discrepancy between those activities is that the heart rate zones have been changed. Even small differences in HR zones can result in bigger changes to your relative effort scores than you might expect. Additionally, we're aware of some differences in RE calculations between custom HR zones and max HR. We're investigating ways to make these consistent with each other. In the meantime, we suggest using Max HR if the relative effort seems too low with custom heart rate zones set.

Changing your HR zones back to what they were will not impact the Relative Effort on past activities, but it will impact your future activities.  Here's a couple of articles I would recommend you check out to find out more about Relative Effort on Strava:

Understanding Relative Effort

Understanding Fitness Scores

Hello Jane,
Thank you for your reply. 
I can add perceived exertion for this workout but I want to know what happened so I can prevent this in the future. 

It looks like that the mobile apps gives the HRzones back which the activity is recorded, unlike the web version were the data changes with the settings.
This give me the info that the HR zones are recorded as are shown in the pictures above.  
Thank you for the links but I had already read them. 

@JasperH You can force the recalculation of the Relative Effort based on the current heart zones by changing the activity type back and forth, i.e. to Ride and then back to Run.

Hello Jan,
Thank you. This helps me.
I get a effort of 27 now. That's more in the direction I am expecting. 

I have tested some changes and I have the idea that the way the HRzones are calculated (based on max HR or custom) is very depending on the relative effort.
When I put my settings back to max HR of 185 I get again a relative effort of 86.
The graph of the custom HR zones is changes what indicates to me that these are the HZ zones calculated by Strava for the specific max HR .

When I activate the custom settings but I don't change them (so they are as above) then the relative effort drops to 27.
I think the differences the the way of calculating the relative effort for maxHR or custom HRzones is different like Jan said in the earlier post, but can have big impact.