Do you have auto save on? If you look in the project folder for the track you’re having issues with there should be a lot of .bak files. If you look at the last modified date and find the most recent version before you opened in 9.5 you can open that and you should find yourself back before 9.5 messed things up for you. Normally the higher the number after the project name on a .bak file the older the file is. You can open a .bak from the cubase menu or on PC you can rename the file to something unique and change the .bak to .cpr, be aware that if you double click a cpr to open it it might default to opening in 9.5 so it is probably better to boot 9.0 and open it from within the programme. I am sure there is also a way to change from .bak to .cpr on a Mac but I haven’t looked at that myself in years.
It is one of those old sayings, don’t update if you are in the middle of critical work, however these days we are torn between having the best tools to be ahead of the game and having a reliable system that works. There are benefits to being on the bleeding edge of technology, especially in an industry as competative as music and audio but there is also a much bigger chance of that technology kicking you in the ass when something goes wrong.
I have been on Cubase for about 22 years and for at least the past 10 I have seen comments about the end users being used as Beta testers. However I do think with a DAW like cubase that can do so much, had led the way in so many innovations and hasn’t dumbed down for mass appeal (like Logic) we can’t really expect every new feature to work 100% at launch.
I would always reccomend keeping important projects away from brand new updates, do a “save as” or back up to a whole new folder if you want to open something in a new update to check it out. I tried to open a project that had caused DOP issues in 9.5 in 9 and it was a mess. I deleted that project and went back to a previous version.
All that being said, DOP does seem more broken than any of the other new features Steinberg has given us in recent years, I feel as if who ever tested it didn’t ever test in batch or with files that might already have different processing on them, I really like the idea of it but at the moment I am not upgrading to 9.5.