I would next recommend running the Validate & Repair tool on the data file from the File menu > File Operations > Validate & Repair option.
In the Validate File window that opens, click the top box to "validate file" and then click OK.
When the validation completes, a data log will open in Notepad, please let us know if any errors or issues are found/repaired, and when ready close and re-open Quicken.
Does the transaction reappear after these steps?
If so, can you please provide what type of account this occurring in and what type of transaction this is? IE. Expense, Income or Transfer?
Is this a scheduled transaction by chance?
Let me know!