Thanks, I can confirm the bug. I’ll try to find out how this could happen. 

Textastic 6 was released as a new app, so you likely never deleted the old Textastic 5.3.1 version. You can safely delete Textastic 5.3.1 (the old icon has a bottom "shadow" while the icon of the new app doesn't).

Ok, that indicates that iCloud sync does not work properly and files do not get uploaded. I’d first try a reboot of the device. 

Ok, then I don't know what's going on, sorry. I'm not aware of any data loss issues in Textastic.

Are you on iOS 13 by any chance?

Is this on iOS 12 or iOS 13 beta? iOS 13 is not supported yet.

Maybe the folder was not uploaded to iCloud yet. Otherwise they should be there on icloud.com.

If your files are stored in the "iCloud" location in Textastic, you can recover them on iCloud.com: 

• login with your Apple ID on icloud.com
• go to Settings on icloud.com
• go to Recover Files in the Advanced section
• there you can select the files you want to restore

Files in "Local Files" can only be restored if you restore a complete iPhone backup.

On iPad, you can still drag a folder from Working Copy into the side bar of Textastic to open it as explained in the manual at https://www.textasticapp.com/v8/manual/integration_other_apps/git_client_working_copy.html#use-drag-and-drop-on-ipad-to-open-a-repository