Hi @darb, removing child sites from your dashboard should not be affected by nuked WP installations. The remove process should still work.
Can you please post the community system report from your MainWP Dashboard for review? The report is located in your Dashboard under Status → Server, on the top right of the page.
Be sure to use the button like the one below; this button hides all your private information:
Pressing the button auto-copies the report to your clipboard then just paste it in a reply here.