There have been a few reports of missing data issues in iCloud with beta versions of iOS 13 and, possibly, macOS 10.15 which can affect Pixelmator documents. This has also been referenced in the iOS 13 & iPadOS 13 release notes. You should be able to get your data back by recovering deleted files on iCloud.com as noted in the screenshot below.
For anyone considering jumping onto the latest the iOS, iPadOS, or macOS betas — our advice is to wait for now. And, of course, if you want to bypass issues like this completely, stay on the stable versions of each OS and wait for their public release in the fall.
A place to talk about anything else with other Pixelmator users.