Using miles for an upgrade is considered an award, just like redeeming for a ticket, and is subject to the same mileage redeposit fee as that as well. So yes, you can get them back, but if you aren't a plat or above, there will be a redeposit fee, which varies by status level.

Not sure where you work or what kind of culture you have there, but if this was an approved vacation that got canceled, I'd find out if there is a policy regarding this. IMO, if the vacation was pre-approved and business reasons force you to cancel, they should probably provide reimbursement for these kind of fees. YMMV, of course. Also, if you have travel insurance, check to see what the terms are and if it would provide reimbursement for your fees - some, though certainly not all, will cover cancellation for any reason.