LodgeiT can pull  "Lodged" Activity Statement from the ATO. It means that you will still have the copy of the Lodged BAS (if you have lodged it via the ATO portal).

This example shows the difference between form that has been lodged using LodgeiT and pulled from the ATO -
 but then, if you still want to do "mark form as lodged manually". Please see below:


Remove the Activity Statement form first in LodgeiT, since you had already lodged the form directly via the ATO portal - How to remove or delete a form?.
Next, import the "Lodged" Activity statement - Pull New Activity Statement.
Once the form is in LodgeiT > Validate the form & clear all errors, form status should be "completed"
Top right of your form, press "Mark form as lodged manually".