Thanks a lot for the detailed info, Engineer 
It seems like it’s getting more and more complicated since with the same program the negative balance is carried over for some accounts while it isn’t carried over for others (Focal Click and WagerShare from your examples).
I also just checked the terms of Cpays:
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4.6 Negative Carry-over
CPays has a negative carry-over policy, meaning that after the first two months, if your balance is negative, it will be carried over to the following month. However, you can avoid the negative carry-over in one of the following ways:
If you are a new affiliate, you can ask in the comment box for a “no negative carry-over account” while signing up.
If you are an existing affiliate, and your balance is NOT negative (0 or positive), you can contact us and ask for a “no negative” carry-over account.
By asking for a no negative carry-over account you are aware that your Revenue Share will be 5% lower than shown in section 4.1 – table A, and that the affiliate commission when having no negative balance carry-over will not be higher than 35%.
Please note that this option is available for active affiliates only, CPays reserves the right to cancel the “no negative” carry-over to an affiliate that does not bring any traffic for over 3 months.
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So, they have carry-over accounts and no-carry-over accounts as well.
I guess the only way to handle this properly is with an option for each program where you can set whether you have a carry-over account or not. And even then it might not be always accurate as your account can change.