It will take 12 or so weeks for the IRS to process your 2016 amended return. It doesn't make sense to hold your 2017 for that long.
Send in your 2016 1040X and also file your 2017 return, based on the corrected 2016 return.
The normal quick checks that the IRS does as part of the initial e-file and loading process probably won't catch this discrepancy (it would catch that you failed to file a 8889, but possibly not that there was a discrepancy between 8889s year over year). That discrepancy checking is often during the year after the return is filed.
If the IRS happens to notice and writes you a letter, just reply that you have completed and mailed your 1040X (give the date) and how it now agrees with the 2017 return; I imagine that will be the end of it.
