As with any techniques using a data hub, you do need to be mindful of the imports to the target models; these should be scheduled "out of hours" whenever possible and the imports should use the minimal amount of data to improved the speed of the import itself.
However, the technique will not adversely affect performance as the list size increases per se. Yes, the more you are deleting, the longer it will take, but that does not mean the technique should not be used. In fact that it is the most optimal way of updating the list in the target.
Deleting and reloading the whole list each time when there are common members is bad practice and will cause more issues than the technique described
All of the Best Practice and advise we post on forums and our other articles on community are based on months of research using a wide variety of models and data structures, and use our internal labs to accurately analyse the effect of different techniques
My intent was only to suggest alternative approach importing only the delta items. Capturing the deletes in source model in a say "archive" list, which would be used to 'delete using selection' in the target model. This will send through only delta i.e. new creates/modified/deletes in the import action and keep the processing of the model optimized.
If you are trying to delete items in Model B with the selection stored in Model A, then you could import the boolean line item into model B first and then use 'delete using selection' to clear list items in Model B. Is that what you are trying?
There is no way you can delete items in model B from any action located in model A. The only way is to go to model B and delete items from there.