Your discovery is not the first time that's happened. I've heard it's a fairly common mistake. Someone performing the 100 mile service probably removed the engine oil and sub-transmission oil drain plugs and refilled only the engine oil.
A Honda service manager told me he's seen it several times. He said me the sub-transmission gears are straight cut gears and pretty rugged. He claimed he's seen a Pioneer driven 100 miles without lube oil in the sub-transmission then refilled with oil and and everything was okay.
Try refilling the sub-transmission with clean oil, drive it a mile or two using high and low range, 2 and 4wd,, then drain it again, replace the filter, and refill with fresh oil. You may get lucky and find that no damage was done.
Worst case - it can be rebuilt with new gears and bearings. It will probably cost around $2,000 for parts and labor.