Hi Wedn3sday,
Thank you for your post and welcome to the Community Forum.
In this matter, both reports should have the same amounts. You can start by checking the set up of the online and manual reports and checking the same tax codes have been selected in both. In Lodge Manually>>GST worksheet, click on the Set up button for the G1 field. In Lodge Online>> Settings>>Set up activity field statements. Then, Run the GST (Detail) cash or accrual depending on how you report, and compare the amounts in that report to your lodgment reports.
After checking and the figures are still different, In Lodge Online, you can open that BAS and click on Update the from Ledger and see if that corrects the issue.
Please let me know how you go, If you need further assistance, please feel free to post again.
If my response has answered your enquiry, please click "Accept as Solution" to assist other users find this information.
Regards,
Cel