Changing versions of CrossOver should not, by itself, destroy any bottles or document files. Those would only have been destroyed if you took specific steps to do so.
Document files may be saved anywhere from a Windows program. Often, it will default to somewhere in the virtual C: drive of the bottle, which you can find by going to CrossOver > Configure > Manage Bottles > Advanced tab > Open C: Drive in Finder.
This is also accessible by navigating in the Finder:
(your home folder)/Library/Application Support/CrossOver/Bottles/(bottle name)/drive_c
It is also possible for a Windows program to save files elsewhere, like in your Documents folder, your Desktop folder, etc. Your best bet for finding the files may be Spotlight or Finder > File > Find.
If the files were around for hours, or perhaps days, then Time Machine should be able to recover them. It would typically only miss files that were short-lived relative to how long they've been missing. (That is, if a file only existed for less than an hour, then Time Machine may never have backed it up; if it existed for less than a day, and it's been weeks since you lost it, then it may no longer be available in backups; if it existed for months, then it should be possible to retrieve some version of it for a long time.) You can use Spotlight/Find within Time Machine to find files if you don't know where they are.