Hi,
Please can you confirm if you are using 1.0.2 as I am not seeing the same issue?
I am testing with v1.0.2 of the plugin and I am using WooCommerce v3.3.4 on WordPress 4.9.4.
I tested the following scenario:
Assigned a product variation to a price band with regular price of £5.00, sale price of £2.50.
Viewed the product on frontend, after selecting the variable options the price is £5.00 and sale price £2.50.
I then edited the price band, changing the sale price to £1.00.
Refreshed the product page on front end, price is still £5.00 but now has sale price £1.00.