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It definitely is doable, I run two different lots of ammo in my 22 and two different loads in my creedmoor, the key is to just not get confused or forget which is which.
Thankfully the difference in...

No issues at all other than if you forget to account for the offset or swtich loads back and forget to un-offset.
Do you actually have the two loads or are you intending to develop a long range...