You can't average percentiles. Period.

Gil Tene on the common practice of averaging percentiles for monitoring:

At first blush, you may think that the hourly average of the per-5-second-interval 99%ile value has some meaning. you know averages can be inaccurate and misrepresenting at times, but this value could still give you some "feel" for the 99%'lie system, right?

Wrong....

If you had the Maximum value recorded for each 5 second interval over a 5000 second run, and want to deduce the Maximum value for the whole run, would an average of the 1,000 max values produce anything useful? No. You'd need to use the Maximum of the Maximums. Which will actually work, but only for the unique edge case of 100%...

The only thing you can deduce about the 99%'lie of a 5000 second run for which you have 1,000 5 second summary 99%'lie values is that it falls somewhere between the Maximum and Minimum of those 1,000 99%'lie values...

Bottom line: You can't average percentiles. It doesn't work. Period.