No, you cannot interchange long and short bolts in your pair of 6.5 CM Savages. If you've physically done it and they seem to fit, then you have two identical length actions, not one short and one long.

If you do indeed have two 6.5 CM short actions, you can use the same bolt in both if you first verify headspace, and you can likely fire factory ammo in them. However if you already are, or plan to hand load, the brass fired from the two chambers should not be interchanged, and you'll have to set up two FL sizing dies, one for each chamber.

While it may be possible, it is generally considered unwise.