File → Copy or Backup File → Create a copy or template, does create a new data file id for the file, along with deactivating all the online services. The data file id is use to connect to the Quicken Cloud dataset, and as such with a new Quicken data file id a new Quicken Cloud dataset will be created for that data file.
This was done to prevent where the old copy of the data file (or if you use Windows copy) the new data file had the same file id, and as such couldn't be used as a separate data file because the two copies would both be syncing to the same Quicken Cloud dataset.
If you aren't going to use the old data file again, yes it would be a good idea to delete the Quicken Cloud dataset from the old data file.
If you are asking whether making a "file copy" from within Quicken causes the new file to change any of your settings for the file - the answer is "no". If you are referring to something else, please be more clear and provide more information.
Frankx
