You will have to update the form elements in the cart from using the display index to using the WAUID instead:
instead of: eCart1_Quantity_<?php echo $eCart1->DisplayIndex; ?>
use: eCart1_Quantity_<?php echo $eCart1->DisplayInfo("WAUID"); ?>
I'd suggest regenerating the cart entirely though. The new cart displays are mobile friendly and responsive and have several other improvements.