I have tried importing transactions via the CSV format, this successfully imports, when I view the history after the import I can see all of the records there.
After about an hour all of the transactions vanish and the records which where in the history have vanished.
How can I debug why the successfully imported transactions appear to revert without leaving any records in the history?
Manager does not do any automation so surely not deleting anything that existed. As @Joe91 asked is how and where you are storing your Manager files? Also you need to explain what Manager edition (Cloud, Server or Desktop), Manager version and Operating system you are using. Also are you the only user and are you only using one or more computers to use it?
Also look at the History files for the transaction types involved.
I also wonder if you are actually completing the import process in accordance with the Guide or whether you were looking at an intermediate screen. And have you checked your Suspense account?
This may be the cause, but there could be more. For example you could import your business in the Cloud version every time you use it or the someone else may reimport backups, etc. You must also look in the Summary page at the bottom of the Balance Sheet if there is anything in the Suspense account as suggested by @Tut. If so then you need to most likely assign accounts to the imported data to reappear in payments and receipts.
@benlongstaff, your screenshots of History are not of much help. You have shown a segment of the History file related to setting up a business, including creating a chart of accounts and defining user permissions. Then you show History for payments. They are totally unrelated, so they do not illustrate anything.
You need to show the History file immediately after what you believe is a successful import. Then show the same thing after transactions disappear. Also include screenshots of the various screens you encounter during the import so we can tell if you are importing correctly.
As @eko reminded you, tell us what you see in the Suspense account, if anything.
I recommend that you do this in a test business rather than you live records.