@uncfnp
Scoot is by far the best connection to MDC (the airport for Lembeh) from Singapore. Everything else requires a stop in Jakarta, and will mean travel will take over twice as long.
Virtually everyone flying in to Singapore (and transiting) will have to recheck their bags if they are flying on Scoot (they offer very limited baggage transit services, and only for Singapore Airlines flights booked on the same ticket).
The process is simple. You will clear immigration in Singapore (very fast), lines are often non-existent, collect your luggage (also very fast), and then potentially have to change terminals using the skytrain (Scoot departs out of terminal 1). This can take ~10 min... recheck your bags with Scoot... (done)
SQ uses terminals 1, 2, and 3 and they vary the terminals for the same flight across days, so you're not going to be guaranteed to know which terminal your landing at until there are only few hours left in your flight (there is a chance you will land at terminal 1 and the transit gets even simpler)
If you are on the direct JFK-SIN flight you are going to have a couple hours to spare (easily). If you are on the flight that goes JFK-FRA-SIN you should have 2.5 hours to make this transit. That should be no issue...
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Scoot is a nice airline, but it is "no frills" - you pay extra for everything. Either plan to get some food in the airport or plan on paying onboard (food is decent - I prefer to bring something with me). The flight to MDC is easy (often ~3.5 hours).