Sorry to have kept you waiting so long. As I said in my last post, I wanted to consult one of my more senior and experienced colleagues.
Sadly he has not been present on the forum, so I've been unable to do so, so at this point, rather than keep you waiting around, I think the best way forward is to explain the options available to us, and let you decide which one you'd like to follow.
1st option ... You restore your server using the same backup as the one you gave me the 2nd Software hive from. We can then (if necessary) replace the Software hive from that with the modified Software hive we've created.
The advantage of this option, is that the Software hive we've modified will "synchronise" exactly with the rest of the Registry, since both were essentialy created at the same time, so there are unlikely to be any "knock on" problems to deal with.
Disadvantage being that your server will not reflect any changes you may have made to it since that backup was created.
2nd option ... you provide me a copy of your Current Software hive, and I strip the CBS hive from the modified hive we've created, and use that to patch your current hive, which we can then use to replace your current one.
Advantage of this option, you do not lose any changes made to your current server since the last backup, and we have minimised (as much as we can) any chances of lack of synch between our patch and the host Registry.
Disadvantage being that minimised does not mean removed, and there may be differences between the two which may cause knock on errors which we may (or possibly may not) be able to resolve.
3rd option ... I provide you with the Software hive we've modified, and you use it to replace the Software hive on your live server.
Advantage of this method is it is quick and simple.
Disadvantage being that because we're replacing more keys, there's an increased chance of a lack of synch with the patch and the host Registry, so the chances of knock on problems increases.
Sadly there is no "perfect" solution. As things stand, your whole CBS hive is absent, and there is no way to repair it, other than to patch it with a replacement from an earlier backup, and doing that involves a fairly unpredictable element of possible risk, whatever we choose to do.
So ..... please read through the above options, and let me know which (if any) you'd prefer to take, and then once you've let me know, I can provide you with instructions on how we'll proceed.