Importing products while Quantity Breaks is active will overwrite important metafield data required for proper operation.
The way the app works is it creates extra variants for the different price levels and if you do an export or import you can override those. Even worse, it can make it so the app loses connection with those items if the import overrides a products metafields... which is almost always the case.
There is a proper way to do it though!
If you need to do product imports all you need to do is remove all your quantity breaks groups before you do the import/export. To do this simply PAUSE your quantity break and wait for the job to complete. Above your quantity break listing you'll see any batch jobs running. Once that's done you're safe to do the import. After you have done your import you can re-apply the quantity break to any items, collections etc, that you like by pressing the PLAY button.