I did it for my 1st cycle which I just finished. Also, I had two overlapping exercises - lat pulldowns and shrugs - between my routines. Eventually, I found which exercises I preferred, so this upcoming cycle I won't be doing the split routine.
The increments would be larger for exercises since you are only doing them three times in two weeks, but all in all you are performing a similar exercise in the other routine so it doesn't matter that much. Go ahead and try it.
-Colby