You should probably try to get the Form 1099-R corrected to show an ordinary distribution (code 1 in box 3, $0 in box 2)). That would eliminate the need to provide any explanation to the IRS. If they are willing to correct the form, they should also be willing to accept the rollover back to the original account. If they refuse to correct the form (which will probably be the case), you'll likely need to provide explanation to the IRS as to why you reported a rollover of what the HSA custodian claimed on the Form 1099-SA to be an return of excess contribution.
