Trinket: Battery + USB at the same time?
From https://learn.adafruit.com/system/assets/assets/000/010/773/original/adafruit_products_trinket3.png?1378223258 it looks OK -- there are blocking diodes D3 and D2 that prevent backfeeding either the battery or the USB +5.

If you are worried, or want to monitor battery-only performance, you could make a special USB cable with the +5 red wire disconnected, and rely on the in-circuit battery to power the device, while still using the USB data lines.  See https://www.pjrc.com/teensy/external_power.html Option 2 for an example of the cable surgery.