Hi Michal,
I have been testing the sub-microflow extraction process in 8.0 this morning, and I am unable to re-create your issue. It could be I haven’t replicated your circumstances exactly. This sounds like it may be a product bug, so you should create a support ticket at support.mendix.com and attach your project to the ticket so the dev team can have a look.
Now it's a known bug of Mendix Studio Pro
(From release notes v8.2)
Known Issues
When you use the Extract sub-nanofow or Extract sub-microflow functionality, the contents of the extracted flow might be lost after exiting Studio Pro. As a workaround, open the extracted flow, make a small change (for example, change the position of an activity), then save manually. (Ticket 88764)