User has a phased project, and the phases are always combined on the invoice when batch billing. However, on adding a new phase to the project, it does not combine with the other phases in the Create Batch Invoice screen.
This can happen if the new phase you added does not have the project rule Send as joint invoice assigned to it. All your existing phases have this rule assigned, which causes them to combine onto a single invoice in the Create Batch Invoice screen. So, you must assign the rule to the new phase if you want it to combine with the other phases on a joint invoice. Check CORE Help Center for details on assigning project rules. You may also want to check out this task that shows how to copy the project attributes (including project rules) right when you create a new phase.