If they paid using a voucher there's usually no way to do a partial refund through ebay. I wouldn't recommend refunding them separately because they could still do a claim and get all their money back, on top of what you've already refunded.  So I'm not sure what the answer is but maybe you'll have to contact ebay.  Not that I'd hold my breath waiting for help from them!  I think the vouchers cause a lot of problems in this respect.

Your restocking terms are nobody else's business and if the buyers read them before they buy, then they either accept them or they shouldn't buy.