There is a foam underlay used for laminate. I know that many vinyl click products do not require the underlay but there is no harm in using it. Add the number of layers of this foam underlay in the low areas to bring it level with the existing tiles. Quick easy and inexpensive way to add the required thickness to the existing floor.
If the levels differ a small amount then likely no issue as the vinyl products have some flexibility. The current difference of 3/8 is too much and would be noticible.