This is a two-part answer.
First, by default, all ward funds remain in the ward. It's possible the stake might ask for any leftover funds, but unless there's a check or a transfer, the ward keeps all funds from one year to the next.
Now, the individual budget categories all get reset on December January first. So all checks must be cut before that deadline. (I'm not sure if it's midnight local time or midnight Utah time - either way, that's cutting it close.) Any check cut in 2017 will be reflected in the new year's budget. Although it's possible to do some finagling (perhaps using a different category or increasing the organization's budget) but that all falls into the category of "complicating things" as well as making the numbers less clear.
One possibility, with the Bishop's permission, is that any balance at the end of the year for each organization will be added to their next year's budget. That would eliminate the "spend it or lose it" mentality. But it may create an issue of setting budgets for the following year since for many people the default starting position is the current year's budget. (Although, that's not the procedure in the handbook - which calls for making a plan and then calculating the needed funds.) Yes, it's a bad procedure, but I suspect it's all too common.
My advice is to set a deadline and tell them they must turn in the receipts to you by a certain date/time. Anything turned in Sunday, January 1st will come out of the new year's budget.
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