Hello,
1. Please ensure all submission processes are finished and files got moved to the pending review section at all agencies before deleting it.
If it does not help try finding some pattern of this issue: when does it happen, what is the common situation/operation when it shows the message that it can't find the file.
If nothing helps, please post a screenshot of the error message.
2. Can you show the screenshot of the error message?
3. It can happen if files are being busy by other operation (uploading, submitting, etc.) and thus can't be accessed for writing.
The program waits for the other operations using the file to finish before proceeding with the file save.