Making changes to the components of a kit in the BOM

I am wondering if there are any negative repercussions that I may not be thinking of if we make change to the BOM for our kits.  For example, we have kits that have multiple boxes in them and sometimes we may decide to repackage this kit and break what was once a single box to 2 boxes.  Or maybe we make a change to one of the components of the kit and it is such a change as to require a new item number but it still keeps the kit the same just need to replace a component/box in the BOM.  My accounting department is claiming this is a huge problem for history but I don't want to change the kit item numbers which are what all our dealer use to order product plus are the SKU numbers for our products on all the partner websites and marketplaces we sell our products.  Anyone able to assist me on this?  Thanks much.