I have a similar approach. What I did to solve the linking problem is to change the Mon/Wed routines down to a single routine with a day of ANY. Same thing for Tue/Fri (assuming you meant Tue instead of Wed in that second group?) Call one Arms and the other Legs or something descriptive so that you know which one is for which day of the week.
It is not as nice in that you have to know what you are doing each day of the week. But at least all the exercises in the applicable routine are tracking so that the default weight/rep values and the last workout values are what you expect them to be.
I suggested something 6 or 8 months ago and it still isn't implemented. I do a 3 day a week program that's a bit different each day but does share squats each workout. It would be nice if what I did on Wednesday would be listed in Friday's workout, instead of last Friday's numbers.