I found out that between two cases (working and not working one) only file that differs substantially is qmlcache_loader.cpp. In non-working case it was over 5 times smaller than normally, and that's because 80% of all resources were not there.

Now, the only reason why it's happened is because some qrc files has been added to RESOURCES twice, and only those resources were available at the end.
Why it worked after moving file from one qrc file to another? Probably because only those part of the project which depends on that two files has been updated and though every qrc file has been included only once (duplicates was in my case in the other part of the project).

EDIT:
Before marking it as solved I will try to confirm all of the above hypothesis.