Hi drpatso ,
Thank you very much for your post.
I am sorry to have issues, however, ATUM free WP plugin has nothing to do with any import tool.
Let me explain:
The free ATUM only shows what has changed in WooCommerce so if your import changes things to out of stock, ATUM will reflect it. You can use ATUM to change the manage stock etc, but I do not think it would cause what you described.
HOWEVER - in case you are importing data not supported by any Import plugin and the data belongs to ATUM there could be an issue, yes.
It would be good to know what are you trying to import and with what tool?