I went to "moved" folder and deleted all the infections(emptied) listed. So maybe it's the reason my folders became invisible.
Is there any chance I can make these folders visible again?..
Early deletion is never a good option as you have none left. So on initial detection send to the chest where they can do no harm.
There is no rush to delete anything from the chest, a protected area where it can do no harm. Anything that you send to the chest you should leave there for a few weeks. If after that time you have suffered no adverse effects from moving these to the chest, scan them again (inside the chest) and if they are still detected as viruses, delete them.
No, this is unlikely to have anything to do with hidden folders, other than malware might have done this.