I agree that it's odd that this major HSA custodian would require you to do the calculation unless the contribution was made to an HSA at a different custodian and was subsequently transferred. In that case the receiving HSA custodian generally would not know when or how much was contributed at the old custodian, so could not do the calculation.
The instructions for Form1099-SA instruct the preparer to use the calculation described in CFR 1.408-11 to determine the amount of earnings attributable to the amount being returned. It's lame of them to push this responsibility on to you, particularly when you don't necessarily know how the attributable earnings might change between the time you prepare the form and the time the distribution is actually made. To be done properly so that the distribution conforms to the law, the calculation really needs to be done at the same time the distribution is being made.
