Hi Amanda,
No, they will not. Well under laboratory conditions they can and in etremely rare instances they can, but in general and in the garden, no. You only need to worry if the variety is actually a subspecies. For example Ipomoea hederifolia var. lutea has yellow flowers. When grown alone and seeds are saved, those seeds will make plants with yellow flowers. BUT if the plant is grown in the same area as Ipomoea hederifolia which has red flowers, the seedlings will end up with red flowers. The red color is in the dominate gene.
Remy