Hi and welcome to the Community 
Cryptomator is not designed for any backp purpose/protection against data loss. You can prevent data theft with it, but for backup reasons I suggest a different solution. (You may browse around this forum, there are some threads using Cryptomator with backup software)
Apart from this, of course your data should not get corrupted during the encryption. Are there any message inside the log files that indicate a problem (like ERROR or WARN) ?
And how do you integrate the cloud storage into your system? With webDAV or just a simple directory watched by some sync application?