"it gives me the its already been reconciled"

That doesn't matter; you are changing the Status of Billable or not. That never changes the Financial reporting of that data.

"I accepted this message once before when doing something else and it did mess things up..."

Even if that Did apply, you can re-reconcile any account. When you are not changing amounts that post to accounts, there typically is no effect on the Cleared status of the Transaction itself. The Billable status is not That Transaction; it is that transaction's Detail or Splits, on the Items tab (and the expenses tab, which really should be done using items, for job reporting purposes).

"If I'm only making it unbillable......" <== Make the changes that Matter to you