Organization is key...
Every piece of content downloaded from DS is renamed by KUID & NAME then stored in a separate folder called... 'Downloaded'.
Then each piece is run through the Content Manager to check for missing or faulty items. When and if fixed (if needed), the content is then moved to another separate folder called... 'Installed'.
Those items that I have yet to fix or are bad are moved to a final folder called... 'Bad'.
I routinely make backups of data from my computer, including content for Trainz and all I have to backup is the 'Installed' folder. If I have a crash or need to reinstall, I know that the content in that folder will 'commit' straight away without need of tweaking.