I think I must retract this question. I notice now you can create a certificate at admin level and then assign it to a reseller's end user, which apparently in this case I did. I changed the end user instance of this certificate from Start SSL to Let's Encrypt, but I should have done that on admin level. I tried now to do it on admin level and it seems to have "taken over" the certificate management although there could be a conflict there.
First of this seems all very confusing and at end user level it should be clearer who in fact really owns the certificate. When admin made certificate then I thing the end user should not be able to touch it or when he does, it should break the dependency chain (remove it from admin).
Secondly I think it should be clearer in the user interface what is really going on here. On the end user side I could not see that the certificate in fact was made on admin level and assigned to the end user (you can only see this on the admin side). This lead me to make the mistake.
I cut and paste the certificates from end user to admin now and it was accepted and then enabled the ACME management on it. I don't know if Let's Encrypt will now accept that management was taken over by the new ID. If this is not possible without errors, LC should warn me or make it impossible to do so (instructing me how to do it right). I then disabled the ACME management at the end user side. I now wait and see what happens next renewal attempt, if it will error out because of ID change.