No, it is not appropriate to involve your national delegation.  Disputes you have with CERN should be resolved via the internal dispute settlement procedures.
First, it is worth attempting to resolve the matter amicably. You may wish to discuss it with your hierarchy, your Department Head, the Human Resources Department or the Staff Association. 
If the matter cannot be resolved amicably, you may challenge the decision within CERN, either through the review procedure or directly through the internal appeal procedure (S VI 1.039). Thereafter, once internal remedies have been exhausted, you may wish to file a complaint with the Administrative Tribunal of the International Labour Organization (ILOAT).