Wow, this is becoming a bigger issue than I thought so.
Its affecting the GL opening balances also. 

Unfortunately I am not that well versed with the SQL side and not familiar with the table structure.
The backups size currently is 18mb.
we have 3 fiscal years deleted. total number of years is 10 years.
How do I journal to the actual customer account?

Thanks.
Is there a solution to fix existing customer balances as I do require that at the moment?
I can also see the same issue on the supplier balances.

Rep102 issue. When deleting old fiscal years it still leaves the old customer payments in the transaction list, though general ledger balances are correct for debtors. But individual customer balances are not correct.

So when choosing the show allocated option as yes, the balances are all wrong as the report is including all the negative balances. Is this a known issue?
Feels quite major as unable to get a aged list which matches the year end balance for the audit.