The bolt you are talking about is one of the item #50's here, right? https://www.partzilla.com/catalog/honda/atv/1986/trx250-a-fourtrax-250/right-crankcase-cover
If so, that is an M6 by 16mm long bolt. Just go to local hardware or big box store and pick up a M6 x 20mm (or so). But if you do put a longer bolt in and it engages with whatever threads are left in the case just fine, make sure that the bottom of the bolt head actually bottoms on the cover. Otherwise it won't seal well (you probably knew that but sometimes we have to state the obvious).
You can also pull out the remaining good bolt to size up for thread pitch and length.