The same thing happened to me.  First of all, I always print to pdf luckily. What I ultimately started to do  was to print the K-1/K-3 for each partner separately using the "choose which forms to print" function.  This also allows me to print fed and state K-1s for each partner to one file.  It works better for me especially when there are multiple states involved.  No collating of K-1s necessary.  But I do have to print each partner separately.

On another note, does anyone have any idea when the K-3 input worksheet on the 1040 level will be available?  My software jus says "in a future version."