Hi Psiamal,
I believe you can just remove that file, then the CM agent will re-generate it with a unique ID for you.
I would stop all your agents, delete the hosts via the CM UI, delete the uuid files on the agent hosts, then start your agents. The hosts should appear correctly in the CM UI shortly.
I don't think there's any other things you need to purge from the clones. Can't say I've tested this myself though.
Thanks,
Darren