Short answer. Yes. Article 1206 draws a sharp line at the moment of substitution: before it, negligent loss or deterioration of the intended substitute does not make you liable, but once the substitution has actually been made, you are liable for its loss through your delay, negligence, or fraud — exactly the situation you describe.
What the law says
But once the substitution has been made, the obligor is liable for the loss of the substitute on account of his delay, negligence or fraud.
Civil Code, Article 1206 — Facultative Obligations. Read the full provision →
What a facultative obligation is
Article 1206 defines the arrangement you are in: when only one prestation has been agreed upon, but the obligor may render another in substitution, the obligation is called facultative. Only the original, principal thing is actually owed; the substitute is simply an option the debtor may choose to use instead. Because only one thing is truly due at any given time, the law treats the substitute differently depending on whether it has actually taken the principal's place yet.
Before substitution: the substitute isn't the debt yet
While the substitute remains only a possible future choice, Article 1206 shields the debtor from an ordinary risk: the loss or deterioration of the thing intended as a substitute, through the negligence of the obligor, does not render him liable. This makes sense because, until substitution actually happens, the substitute was never the object of the obligation — the principal thing still is — so its accidental or even negligent loss does not touch what the debtor actually owes.
After substitution: it becomes the real object owed
The moment substitution is made, that protection ends. Article 1206 continues: once the substitution has been made, the obligor is liable for the loss of the substitute on account of his delay, negligence or fraud. Handing over the substitute in place of the original prestation converts it into the actual thing due under the obligation, so ordinary rules on liability for fault or delay attach to it from that point on, exactly as they would have attached to the original prestation.
Applying this to a delay after substitution
On the facts you describe, the substitution had already occurred before the damage happened — the substitute item was handed over to replace what you originally owed. Article 1206 puts you squarely in its second sentence rather than its first: because your delay caused the loss or deterioration after substitution, you are liable for it, even though the same negligent loss would not have made you liable had it happened to the item while it was still merely the intended, unexercised substitute.