Encoding of genotypes is confusing and error prone

As I understand what I've done, genotypes in 2-way RIL should be coded as 1 or 2.

But for multi-parent populations, I'm assuming SNPs coded 1/2/3, and so inbred founders should have codes 1 and 3, and then offspring lines (4-way RIL, 8-way RIL, etc) should similarly be coded 1 and 3. If someone uses the codes 1 and 2 in this case, is there a warning issued or are the results just messed up?