If you wipe the server, there is probably very little risk of someone getting your private key or certificate, so relatively safe ( in that you can’t revoke the old certificates without your account key, but you probably don’t need to if everything was removed beyond use).
There is a limit to how many certificates you can have ( 5 / domain / 7 days - this includes subdomains)
If you are doing it every day, that would be a problem. If you are doing it once a week, from the technical viewpoint of your server / SSL it wouldn’t be an issue for one domain.
However, having said that, I like to think about LE, who are very kindly providing the free certs, and I don’t think it’s particularly nice to them, loading their servers, repeatedly asking for the same certs if it were on a frequent basis.