I am having similar problems but I think I have messed things up much more, trying to figure this stuff out. I have a moderately complex set up and I am hoping not to start over from scratch. I have plugged my way through many of the helpful posts and how-to's but am still stuck. So either I have pooched things up severely or I am missing something in the various steps and permutations.
Symptoms: some of the lighting/switch combos are still working fine (those that do not need a Scene or Program, eg. switch pairs etc). But I have been unable to restore my more complex settings.
Longer description of what I have tried: initially, I thought it was the ISY994 that was on the fritz. I did not catch the importance of the PLM in my brief readings of the forum (stupid me!). Replaced the ISY and tried to restore settings etc before I realized that it was the PLM that was the culprit. I then replaced the PLM, but again stupidly did not follow the proper steps (thought it was just plug/play/swap) so in reconfiguring the ISY, I think I now have a godawful mix of settings between old and new PLM parameters. And of course, the ISY Backup from 2 years ago when all was working swimmingly died on the hard drive 6 months ago. Sigh.
So currently, after much messing around, with a much more careful read of the various tips, I am still stuck. In the Main tab on the Admin Console, most of the device names are there, some accurately report current device status but most do not; a few will allow simple commands such as 'Fast On' but most will not. And still none of the Scenes or Programs work.
I have tried Restore Modem; Restore Backup; swapping the two ISY controllers and more Restores; and various permutations on reset/reboot order.
So, if I understand correctly (and that is a big and doubtful IF), I think that my current config may have a mix of settings. But if it was just mixed PLM settings, Restore Modem should fix that.
Since there are lots of devices on the home network, I would rather not start over from scratch. Since most of the basic switch parings still work correctly, I am hoping to be able to read from them back into the ISY configuration. Ideally, I would like to keep the Programs and Scenes or be able to restore them somehow.
Hopefully, one of you can suggest a less painful way for me to restore a rather messed up system. If anyone needs an incentive to provide a helpful fix, from what I am reading in the earlier posts above, I am happy to send them my old dysfunctional 2413S, as it probably just needs new capacitors.