Hey there, osmiputnik.
Well if everything's there and working OK, that's the most important thing. The storage space might have been used up by temporary files or by system restore points. If you want to know what's taking up your space and regularly check the amounts of different files so that you could track any unusual activity, you could take a look at this article: http://www.howtogeek.com/125923/7-ways-to-free-up-hard-disk-space-on-windows/. I know it says "7 Ways To Free Up Hard Disk Space On Windows", but when you scroll down, there are a few software options offered, which would help you monitor your storage space. Other than that, I'd recommend that you run a full scan with an anti-virus program (with updated database) and do the same with an anti-malware program as well, just to be on the safe side.
Hope that helps.
Boogieman_WD