The future EASA-based certificate for European aerodromes shall only address the aerodrome safety part of the former (ideally ICAO based) national certificate; as such it does not affect the non-safety related elements which may form part of such certificate/ permit/ license.
The EASA rules mirror the ICAO Annex 14 rule content 1:1, apart from a few exceptions about which EASA Member States are informed through a comparison exercise called EFOD (Electronic Filing of Differences).
Moreover, it is at the discretion of the Member States to decide how to insert the new certificate into their own legal structure: it may replace the former (safety) certificate or come in addition to it. By no means, however, should the insertion of the new certificate impair established privileges and legal finality of non-safety aspects. Recital 9 of Regulation (EC) No 139/2014 should be kept in mind:
(9) Regulation (EC) No 216/2008 only concerns aerodrome certificates to be issued by Competent Authorities in so far as safety aspects are concerned. Therefore, non-safety related aspects of existing national aerodrome certificates remain unaffected.