Should the amount the uncle claims as a debt from the deceased be repaid, even though it was a end-of-service gift?

You are not obligated to repay what your paternal uncle claims was a debt owed by your father, unless he provides evidence for his claim. This is based on the Prophet's (peace be upon him) saying: "If people were given whatever they claimed, men would claim the blood and wealth of others. But the burden of proof is upon the claimant, and the oath is upon the one who denies." This is especially true since you mentioned that he gave the money as an end-of-service payment, and people bear witness to that.