You are syncing HRM Pro with what?
Why you don't have paired your HRM with Edge?

I would say it is some problem with hart rate zones you have set on device you are syncing with.

I synchronize HRM-Pro Plus with Garmin Connect android App via bluetooth.

HRM-Pro Plus is of course paired with Edge 530 and works perfect.

Garmin has the "Physio TrueUp" feature, if I record on more devices the same time, it calculates the correct values.

I recorded my workout with 3 devices and the result does not work.

HRM-Pro Plus delivers almost the double of calories.

Than you have an answer. 
if you teach your workout on Edge with HRM connected you don’t need to transfer same data from strap through GC. 
It only cause double data and result problem you observe. 
BTW. HRM Pro itself is not compatible with Physio TrueUp option, it works only with these devices: support.garmin.com/.../

Garmin advertises, if I make a break during a ride, then the HRM-Pro Plus records the heart rate, even if I stop the edge recording. E.g. 3 hours ride, with 20 minutes pause will be recorded on the HRM-Pro Plus.

On the edge only the 3 hours ride.

After synchronizing everything, the complete calories burn should be accurate incl. the break times.

But not doubled!

I will repeat, HRM Pro is not compatible with Physio TrueUP function.
Reading same data second time you adding more than you want.
GC will mix up all, especially that you collecting HR data through your Forerunner same time and which is Physio TrueUP and gap in HR data should be recorded ob it.

If I dont wear the fr255, I have the same symptoms:

E.g. I start a 3 hrs ride with edge 530 paired with the HRM-Pro Plus, i make 30 minutes pause and stop the edge recording.

At home I synchronize the edge 530 and after that the HRM-Pro Plus.

Because I wish to have accurate caloric values also during the break. (since the edge 530 recording was stopped)

So promises garmin.

But after HRM-Pro Plus sync the calories doubles almost.

Garmin's own HRM Pro+ pages list the device as capable of syncing calories using physio trueup: https://www.garmin.com/en-US/p/770963#specs

(Near the bottom of the page.)

Yes, but other page I've showed earlier doesn't.
It look's that some of these pages are outdated.
I also cannot find option how to enable/disable Physio TrueUP for HRM-Pro or my watch in Garmin Connect mobile or Garmin Connect WEB.

I have also observed that the HRM Pro plus overestimates the active calories if there is no activity recording on the watch. 

The case is when you wear the belt alone, with or without the watch on your wrist, but no activity has been started with the belt recognized as the HR sensor.

It could be that in that configuration, the HRM Pro or Connect app is putting all the resting and active calories in the active calories bucket. That would explain why the number is way too high.

I tested this recently doing surfing. For 2 similar sessions, the HRM Pro plus solo gives me about 1,000 active calories, while an offline recording activity with a post activity HR download gives me only about 300 calories of 2-3h