There is no definition for the word "flight" in the FARs. I'm not aware of any FAA document that clarifies their intent.
The closest I was able to find was only tangential: Clarification of Flight, Duty, and Rest Requirements. In that document, there is discussed "flights" and "flight segments". As an example, there is this passage:
SWAPA provided an example of a 4-leg FDP with a 9-hour flight-time limit in which the crew realizes, after Leg 2, that their total flight time will be 9 hours and 5 minutes if they complete the remaining two legs. SWAPA then asked whether the fligthcrew can depart on Leg 3 of this FDP. In response, the FAA notes that if completing Leg 3 of the scheduled FDP will not cause the flightcrew to exceed the 9-hour flight-time limit, then the flightcrew can take off on Leg 3.
This is typical, where "flight" is mainly used as an adjective, and "flight segment" or "flight leg" (or even just "leg") is used as the noun to describe the actual activity. This example seems to suggest that each leg is a separate flight.
There is also, of course, the definition of "flight time", mainly used to govern logging:
Flight time means:
(1) Pilot time that commences when an aircraft moves under its own power for the purpose of flight and ends when the aircraft comes to rest after landing; or
(2) For a glider without self-launch capability, pilot time that commences when the glider is towed for the purpose of flight and ends when the glider comes to rest after landing.
It could be argued logically that if the time of flight is only that time between starting to move and finally coming to rest after landing, that the actual flight is itself just the movement between those two moments in time.
That said, the FAA is granted broad latitude by the NTSB (the primary adjudication body for contested enforcement actions) in their interpretation of their own rules, and it takes a very dim view of actions taken by pilots that can be perceived as intended solely for the purpose of circumventing those rules.
It is my own opinion, worth every bit of money you paid for it, that your example would not be considered legal as stated.
The fuel minimum requirements would most likely preclude a scenario where a fuel stop was actually required after 40 miles when the next point of landing is only 40 miles further. It's theoretically possible of course, depending on the fuel state at the first departure, but highly improbable. So, lacking a clearly compelling reason to justify the fuel stop after 40 miles, the stop would be viewed as a transparent attempt to avoid the rule.
Now, all that said, that's not to say there's no chance you couldn't get away with it:
- The rule is, presumably, designed to ensure the safety of the passengers by preventing the pilot from having to navigate beyond their training in potentially deleterious conditions (i.e. where the weather is less certain). "Resetting" the navigation with a landing after 40 miles does seem consistent with achieving this goal. If the commercial pilot can be considered competent for any flight 50 NM or less, then surely they are competent to complete two flight legs of that distance, such that they are always starting from a clearly-defined reference point (i.e. the airport where they landed).
- A much more probably-legal scenario would be where there are different passengers for each leg, at least in part. In that case, then there's a clear justification for the interruption of the flight just short of the 50 NM limit. Indeed, one could try to use this scenario as justification for any other "break the flight into multiple legs" scenario. After all, if this more compelling scenario is legal, it's hard to see how other scenarios that are operationally identical regardless of the specifics would be not legal.
All that said, it behooves a commercial pilot to behave cautiously and always with both the safety of their passenger and compliance with the regulations, two things not always directly in correlation with each other. Given the FAA's power to suspend or even revoke commercial privileges, and given the relative lack of recourse by the pilot to reverse decisions like that (it happens, but rarely), the best thing to do before attempting this sort of thing would be to contact the local FSDO and just ask them.
With an official opinion in hand, one will know for sure how the authorities who might or might not cite a pilot under that regulation will actually treat such flights.