Hotfix and Upgrades will only affect /libs directory. So, any workflows under "/conf/global/settings/workflow/models" and the corresponding runtime models under "/var/workflow/models" will not be overwritten.
Example: customized version of the Dam Update Asset will be stored at the paths below:
/conf/global/settings/workflow/models/dam/update_asset
/var/workflow/models/dam/update_asset
So, If you want to move this workflow to another instance, you can create the package of the above 2 nodes. Similar steps can be followed for other workflows.