Let's take example of product design.
This process is not carried out at manufacturing site, but headquarter, which is located e.g. abroad.
It is example of remote supporting function.
Second manufacturing site was established.
Part of current production was transferred from first to second manufacturing site.
Headquarter designed product change affecting one of products made at second manufacturing site.
Now, it's important to follow product design process flow.
Proper sequence is headquarter (product design changed) -> manufacturing site 1 (process design changed)-> manufacturing site 2 (manufacturing changed).
No direct system process interaction between headquarter and manufacturing site 2 is allowed.
Going back to example of maintenance.
No, it's not violating EMS status, that maintenance activities are carried out on EMS, but...
Process partially (Deming's cycle Do and Check) can be made there, but authority and responsibility for "the rest" (Plan and Act) is limited to Top management of manufacturing site 1.
See "Certification rules" Annex 4 - Eligibility for certification structure
Crucial point is "autonomous decision making authority" - it can't be given to personnel specific for extended manufacturing site.
I do not know how did you document it.
From my experience - certification body sometimes have own "add-ons" not based on "rules" and refuse to accept EMS structure.
Then you can't fight this, even auditors being later there to audit, agree with you.
These are internal CB rules, so choice is pay twice for separate certificates or look for another CB.
