Fixing a mistake in a paid invoice

Jetta_D55

An invoice of $220 was paid with a check of $286. My partner marked the invoice as paid and refunded $66. Now there is a check deposit of $286 that is not associated with the invoice. I believe he should have paid the $220 invoice with the $286 check, leaving a credit. Anyway, I don't know how to fix this. The money is right in the bank, but it's left an error in Wave.