Well, yes, you can "pre-emptively" enter the phantom 1099-SA, but you had better write down what you did and why, in case there is ever an audit.
My concern is that your HSA custodian decides not to send the 1099-SA to you or sends it to you next year, in which case your tax return and the IRS's records are no out-of-sync.
Note that you are going to get a special 1099-SA next year anyway, for the earnings on the excess while it was in the HSA. Enter this and the earnings will be added to Other Income (as it should be).
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