Everything that you have in db/data folder will be played by NinjaTrader market replay. However if you delete either .ntm or .nt2 corresponding files you will get only one stream. Very easy task if you need that for 1-2 days, however if you want to get rid of L2 data for 90 days you, probably, need to use some tools for that.
For manual testing using L1 & L2 data may produce funny market depth behavior due to a granularity of 1 second when NinjaTrader merges both data into one stream.
You don't need L2 for manual testing for the above reason and market replay will work slower.