I tried to duplicate your problem, following your steps exactly. Expense B does, indeed, disappear from Customer D’s balance of Uninvoiced items. The
Billable Expenses register shows it as invoiced. But drilling down into
Billable Expenses from the
Summary, no assignment to any invoice is shown. And
Accounts receivable does not include it. But it does not appear on Customer C’s invoice with expense A. That fact seems a little different from what you describe, but I may just be looking in more detail than you did.
I repeated the experiment without the cloning step. That is, I simply entered the two billable expenses via separate spending transactions. Done that way, there is no problem.
So the issue definitely arises only when the expense transaction is created by cloning. This is a puzzle for @lubos.