I don't think there is a right answer. Just keep some kind of documentation that you can use to give the IRS a roadmap of why/how funds were moved. Receipt and contemporaneous notes should work. If your HSA/Payflex account offers an online mechanism to save/upload pics/receipts, you could certainly use that. I'm a tax lawyer, and I don't even keep sophisticated records in this area. Just a manila envelope filled with my receipts and a handwritten ledger of reimbursements Even with all the enforcement money being pumped into the agency, I don't think the IRS is going to be pushing any resources into looking at whether a few HSA charges or reimbursements were proper. There's going need to be other significant flagged issues for them to even start an examination.