It's not a big deal. You could have multiple checking acvounts at various institutions all at same time and QB would warn you about duplicates so you just accept the warning and the duplicate. You might depending on version be able to shut off the warning.
What you could do is order new checks that start at 1001 , there is nothing magic about starting at 101 in fact it is a dead giveaway that it is a new account.
If you have not opened the new account yet the bank can order your first checks with any starting number you want