I seemed to have read that in such contradictions, these ambiguities are resolved in the favor of the one who didn't draft the documents ie the employee in this case. But i'm also surprised HR wouldn't discuss with their legal counsel.
I would assume that signing a (legally valid) variation of your contract would override the company policy - Though it is a shockingly bad oversight on HR's part maybe the CEO ought to put the HR director and or the General Consul on a Performance Improvement Plan.
