We have the following options, if anyone sees a better solution please let us know:
1. Refund him from our reserve and risk setting a dangerous precedent while also risking taking the hit ourselves in case we were lied to. (The Note would remain valid because we wouldn't know which one to delete)
Yes, if you do this, it would really be a precedent and you risk an increase in the number of similar cases. You are literally opening a bug for potential fraudsters. I don't think it should be done, because the rules are clear and everyone should take care of their money.
Certainly, additional attention should be paid to how clearly the essentiality is emphasized to the users to save Note Private Key and Letter of Guarantee.
2. Temporarily disable all Notes with similar balances and wait for the other Note holders to contact us to reenable them. If after some time 1 Note remains unchanged and we didn't receive any inquiries about it we would assume it belongs to this users and refund him. We would still risk taking the hit ourselves because the remaining Note holder may just not pay attention to the situation and not inquire about it only until after we've refunded. This is another dangerous precedent which we would like to avoid at all costs.
This is also wrong because it will cause a lot of additional work for you, checks, apologizing to users, etc... All this can only negatively affect your reputation. Plus, I believe that not all of your users are necessarily active on Bitcointalk, so they are not necessarily familiar with this problem.
3. Treat Whirlwind as a network and respect the rules, in this case we will not be able to help in any way and the user would lose access to his funds assuming it's true that indeed he lost the private key
I don't know what the amount is, but this is probably the only correct solution.
If you still insist on going out to meet the user, you should not hurry with the decision. I would do all possible analyses in detail, even if it took a long period of time.
Just my 67 sat, which is the current fee.