Thanks Perter,
Its very strange, the software responding well, showing the alignment report , doing inspection and stuff and even “allow” to save the project - BUT big BUT it does not really save it in the location that I pointed - just doing a fake save 
So I pushed the Pause button and let’s see how it will respond…
5 min passed and nothing , I’ll giver it another 20min and then kill it.
ooo after 7 min it paused 
Still not saving the model, temp model not updated and the log file on the line of part 17/29…
Update:
After pausing and resuming it seems like something working (there was writing process in the Disk and a few new files appeared in the Temp folder but they also disappeared “etilqs_******…”) but it didn’t work (I gave it a half an hour).
So I aborted the process and the project has saved like 7 times (seems that when you press save it enters to a Que).
I changed the Reconstruction Region and pressed Normal Button again!