a lot depends on how your individual loan accounting system works -- the requirement usually is that the book balance on the GL has to be reduced before you book income.
E.G: ITI has a feature where you can post payments so that the note always shows the contract balance whereas the GL reflects the book balance. If the loan comes off non-accrual, then there is maintenance that can be done on the individual note level to increase the book value and book the income
other LAS applications may have similar features -- it is just a question of finding a guru who can tell you how to work it. If worse comes to worse, you can track the payments in EXCEL
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IMNSHO, FWIIW