Hello,
1. You say that you found the procedure above confusing. Out of the four steps, which ones are you having trouble with? I can help clarify. This is the correct procedure.
2. If you did not perform the above procedure, then what did you do? You say that you cleared the transactions table after migrating the database. This alone would create the problem you describe. You would need to reimport the exported csv files, then enable the new site once you are 100% sure that everything is correct.
3. I am not sure what user meta you are referring to. There are no user meta involved in this. The data is in the transactions table.
The plugin periodically rediscovers old deposits. If you have deleted a deposit row, eventually it will get re-discovered, and you might face the same problem again, until you perform the migration as described.
Please ask me any questions you need in order to understand the migration process. Then you can repeat the steps and I’m sure it will work.
with regards