What can I do about a missing row of tiles when preparing a floor for vinyl planks?
I would not pour anything there.  The chances are it will not be exactly level and may get on our under existing tiles.

I suggest you glue down some pure vinyl tiles right next to it with the same height.  Then when you lay your floor the pattern should be crossing the current pattern.  I would also suggest a good underlayment for you vinyl planks that should hide inconsistencies but the ability to use underlayment vary by manufacturer - but you can call them and even if it is outside their specs.