MacBook Pro (2017) Flashing Question-Mark Folder

2017 MacBook Pro with 128GB flash storage running on Mojave.

Couple of months ago I noticed a blinking folder with question mark when I opened the lid of the laptop - switching MacBook off by holding the power button and on again solved the issue by the time. Little by little it started to happen often and it did not get solved if I just restart, instead had to clear NVRAM, then had to start in safe mode and then restart back to normal mode, and today it did not even boot in safe mode - just the blinking folder and after so many tried it booted normally. I used to shut down every time lately because then it started normally when I turn it on, but recently even then it showed the blinking folder. Also sometimes during screensaver when I click it shows me the login screen, but it is frozen and curser changes to busy and after few seconds the flashing folder appears.

I have noticed when trying to recover when blinking folder is appearing, my full hard disk is not detected in disk utility. I could only see the recovery partition (I guess) with the size of merely 3GB, when I check during successful startups I could see another hard disk or partition that has the running OS with around 100GB.

This is really frustrating, and the warranty just ended a month ago. This issue started in High Sierra, then I upgraded to Mojave, and after couple of days again the blinking folder. Please let me know how I can fix this.

Thank you very much.