I don't believe you were ever able to stop a recording in dual mode across tuners even before the software upgrade. If we're talking about the same thing I can recall many times I was recording a show on TV2 but wound up watching it on TV1 at the same time. When the show was over (but there was still a few minutes of extra recoring time) it would always give me a message that I couldn't stop or delete the recording if I treied (from TV1 anyway).
as is currently.. you have to delete the timer... it will prompt you that the timer is currently recording.. and answer yes to stopping that recording.. *then* you can delete the program. And then too you'll have to re-create the timer if you want the timer. (ie. New Episodes)
The "Stop Rec" button use to appear for me, when I'd go into a recording in progress on Tuner2 .. ie bring up dvr, open and start playback of that Tuner2 recording, then go back into the DVR button, back into that dvr event, and the third button down *use to* change to "stop rec" ... perhaps that was a "feature" before L685 on the 722k ... and when they rolled out the firmware updates (with past 2 versions L683/L685) they may have pulled that option *out of* control from TV1 and made it so that Tv1 could only get that "Stop rec" button on TV1/Tuner 1 recordings in progress while in dual mode.
And another way.. if you have Sling features.. (Sling adapter or 922) is to open up Dish Remote Access ... View Live TV, and then change the channel there... wait for a minute and it will come back with "this will cancel the recording do you wish to continue" ...
In any case, its not as easy as using Remote 2.. but it can be done .. and this would be a "feature request" now to dish.. to make the Stop Rec button appear *regardless* of which tuner is recording and regardless of Single/Dual mode.