Hello J.PB,
As Vaishalee Parkhi & Pon have mentioned, in addition to giving the complete organizational info to this Forum to advise, pl also enquire on the facts of the case.
Another aspect is, assuming you have a formal HR policy in place for Annual Appraisals, even the Manager is bound to follow them.
If the employee is not liked by him/her on performance grounds, then I am sure the employee needs to be counselled & in the worst-case scenario packed off--AS PER THE LAID-OUT POLICY, NOT as per the whims & fancy of any official.
And if the employee is not liked by the Manager on personal grounds, HR has every business & right to intervene--the Focus being the Larger Company's interest & not the manager's.
From the Financial angle, it's the Company which is bearing the salary of an employee--NOT the Manager. So it's neither the Manager's prerogative nor right to waste company resources on a unfit employee.
Frankly, if I were you [& you have every right as HR to ask such queries], I would first question the Manager for sitting on the issue for 3 years without deciding either way. Based on this one fact alone--that you mentioned--I think there's something more than meets the eye w.r.t. the manager. Pl make your checks [if need be, discretely] & figure-out.
If you answer the issues raised by Vaishalee Parkhi & Pon, more accurate guidance suggestions could follow from the members.
Rgds,
TS