Workspaces disappeared after update to Ver 16

It sounds like you did not use the option to "Import previous settings and preferences" when you installed the update to InDesign. If that was the case then the program was installed with all of its default settings thus losing your custom workspaces which are housed within InDesign's preference folder. Despite the fact that you now have lost those workspaces this could actually benefit you in the long run. Importing old preferences when updating can often lead to poor performance going forward. My suggestion would be that once you have set everything back up as you like it (do it with no documents open) quit the program and your new preferences will be established. Then make a copy of your preference file and save it for any future times when preferences need to be reset. Then all you have to do is make a copy of that and replace the corrupt preferences with it.

To find the preference files on a Mac:

The User Library folder in which InDesign’s preferences are stored is hidden by default on most Macintoshes. To access it make sure that InDesign is closed and click on the desktop to launch a Finder Window (Command-N). With this window in column view follow the path User>Home folder (it’s the folder with an icon that looks like a house—it may have the user’s name rather than “Home”) and click on the Home folder. With the Option Key pressed choose Library from the Finder Go Menu. “Library” will now appear within the Home folder. Within the Library folder find the folder called Preferences and within that you are looking for the folder called “Adobe InDesign.”

To find the preference files on a PC:

On Windows 7 and above the preference files are hidden. To find them go to the Control Panel and open Folder Options and then click the View tab. Then select “Show hidden files and folders” or “Show hidden files, folders or drive options” in Advanced Settings. The folder you are looking for is at the end of this path: C:\Users\<USER>\AppData\Roaming\Adobe\InDesign.