Vasek,
Are you referring to files that were stored in a 'Creative Cloud Files' folder on your PC, and synced to Creative Cloud?
Are all the files missing, or only some of them?
Could you send us your log files so that we can take a further look at this?
Please follow the instructions on this page:
https://helpx.adobe.com/creative-cloud/kb/cc-log-collector.html
Then email the logs to syncforum-communication@adobe.com
Thank you,
Ben