Short answer. Yes, for purposes of settling his estate a long-absent, unheard-from person is presumed dead once the Civil Code's periods have run. If he later proves he is alive, he can recover the balance of his estate, after debts, by motion in that same proceeding.
What the law says
For purposes of settlement of his estate, a person shall be presumed dead if absent and unheard from for the periods fixed in the Civil Code. But if such person proves to be alive, he shall be entitled to the balance of his estate after payment of all his debts. The balance may be recovered by motion in the same proceeding.
Rule 73, Section 4 — Presumption of death. Read the full provision →
A presumption limited to estate settlement
This rule does not declare an absent person legally dead for every purpose. It creates a presumption of death for the narrow purpose of allowing the estate settlement proceeding to go forward: once someone has been absent and unheard from for the period the Civil Code fixes, the estate case can proceed as though the person had died, without a death certificate or judicial declaration of death being produced first. The presumption exists because an estate cannot simply sit unsettled indefinitely while heirs wait for proof that may never come, so the rule lets the special proceeding move forward on the strength of the absence itself rather than requiring the heirs to first obtain a separate judicial declaration of presumptive death.
If he turns out to be alive
The presumption is rebuttable. If the absentee reappears and proves he is in fact alive, he does not simply lose his property to the estate that was administered in his absence. He is entitled to whatever balance remains of his estate after all his debts have been paid, and he can recover that balance by filing a motion within the very same proceeding, rather than starting an entirely new case. This protects the returning absentee without unwinding a settlement that the other heirs and any creditors relied on in good faith, since only the leftover balance, not the specific property already distributed, is what the rule guarantees him.
Why 'balance' and not the whole estate
The rule protects the returning absentee's residual interest, not every peso that ever passed through the estate. Debts validly paid out of the estate during the settlement are not clawed back; what the absentee recovers is what is left over once those obligations have already been satisfied, reflecting that the administration was conducted in good faith on the presumption then in effect. This structure reflects a deliberate balance: it does not punish the heirs or the estate for having proceeded on a presumption the law itself authorized, while still making sure the absentee is not left with nothing simply because he happened to be unreachable when the estate was settled.