I'm going to go a bit against the grain here. The ECU has a little bit of adaptability programmed in and can deal with mild changes like going to a set of slip ons. A 2 into 1 system is a little bit more dramatic though and could use a slightly different tune.
Fortunately the Indian performance filter (which is offered by Indian, same shape as the regular air box without the sound baffles and has a K&N style element) comes with retune card. The tune cards are basically an ECU update performed at the dealer. If you have a 2 into 1, the Indian performance air filter is a decent option and it may be enough to keep the bike running well. I would try that first as the Indian performance filter is pretty affordable and the retune it comes with can be enough to get a freer flowing exhaust to run well.
Full Disclosure, I own a 2017 Scout with a RPW 2-1 system and the Indian Performance filter. It runs quite well with the tune on there that came with the filter. I do get the occasional pop on downshift but it's very infrequent and it just adds a bit of character to the exhaust. I am in the temperate northeast though, so your mileage may differ if you are in a much hotter or drier area.
I wouldn't go to an aftermarket Tuner box unless you absolutely had to, which I do not think is the case for just a Bassani 2-1 exhaust.