I have come across this problem and what I do is instead of the two crotchets I put two dotted crochets and then increase the tempo by 1/3. I have attached a work in progress < Beethoven's Emperor concerto where in bar 41 you have to play 7 notes in the right hand to six in the left and you can see how I get round this by adding an extra bit to the left hand and increasing the tempo by the same ratio. I hope this helps.
How do users cope with the direction una corde? Noteworthy has a shortcut for the "loud pedal" but none for the "soft pedal" not to mention the middle pedal. Btw I have a huge selection of piano music all sequenced over 20~+ years using Noteworthy . You can see it all free at http://www.malcolmdale.com
I am currently working on Liszt's Hungarian Rhapsody No 2 and on page 7 comes the instruction "una corde." On a piano this means pressing the left or "soft" pedal which moves the strings so higher notes which are usually played on 3 strings at once are now played on one string (in Italian una corde), but how can I do this with NWC? Any help would be much appreciated.