What i did the last time was to open the eCart object, go through the Columns and Calculations tabs and make note of any new columns that had been added, and any new calculations that had been added.
If there are discounts, charges or tax rules set up that you want to keep, make not of how those are configured as well.
then go to the WA_eCart folder and delete the eCart object file.
next recreate it using the same name in the eCart object editor, and add back any custom columns,,calculations, discounts, charges or tax rules that you made notes of.