Is it possible to flag a selection of customers in some way so that when exporting the customer details as a report, I can differentiate different groups?
In the customer detail report, there is not a way to pull through different groups
Potentially if you use custom fields and add a name in there for a group you could add in that column but then you would have to export the report to excel and then use excel to group them
You do have the option of using class/location on transactions(depending on the package you have) and running transaction detail by account report>you can group by class>then go to customise>rows/colums>change columns>put a tick in the customer. Then you can use the filter to filter transaction type to invoice and any other filter you need to add on.
This may not be exactly what you're looking for.
Feel free to come back here if that doesn't match what you would like.