Skyteam can interline on different ticket and if your first leg is China Airlines i'd say they'll try their best of ability to help.
Even if you aren't able to through check, 3.5 hours is plenty for a self connect with baggage pickup at TPE. Immigration probably take about 30 to 45 mins and you'll have your bag by then. Departures is just 2 floors above arrivala and if you need to switch terminal the train ride is only about 10 minutes.