No, once you confirm it will not prompt again. The Batch Size refers to SQL paging in the queries that it runs. When deleting a huge number of computers, you may get faster deletes by increasing the batch size, which may come at a cost of RAM or CPU usage.
I haven’t seen the transaction log as a problem, but if that really is the case you could force smaller sets of deleting by setting a longer number of days for history cleanup - for instance start at a year, then 10 months, then 8 months, etc. until you get to your target retention period.
Recently worked with a deployment that had been active since Bigfix 6 or 7, upgraded over the years and never had cleanup run before. Had billions of rows to delete, and we ended up increasing the batch size to something like a million rows at a time to get better performance, and started by deleting everything older than, I think 3 years, and worked our way current from there.