The present is never changed for the lab team because they never traveled through time. To our knowledge, the members of the lab team all originated in the timeline in which the time travelers arrive, which is never the timeline the time travelers originated from.
The trio who travel in the time machine, to our knowledge, all originate from the original timeline ("Present"). They go back in the past, change something, and come back to a modified future ("New Present"). They aren't coming back to the lab team they left in "Present", but are coming back to a lab team in "New Present", who only know the history of "New Present" as fact.
In each "New Present", regardless of what happened in the prior "Present" or
"New Present", because people from the future went into the past, the entire timeline has been changed. The constants we know are:
- a trio of people from that timeline "New Present" were sent back into the past
- a trio of people (our main characters from "Present") have come back from the past, having originated from the previous timeline, which might have been another "New Present".
Unlike some time travel theories where time travelers are "unmade" due to paradox effects on a single, malleable timeline (example: Marty McFly from "Back to the Future" starting to disappear in the 1950's when his parents weren't a couple), "Timeless" appears to maintain that returning time travelers do not originate from the arrival timeline. When these travelers come back to the present, they are arriving in a new timestream where the memories they know as fact may or may not have existed.
This type of time travel rule can (and probably will) result in a scenario where if the trio (originating from "Present") conduct actions in the past that erase their own history, when they arrive at "New Present", they will not be recognized as the team who were sent back in the first place!
Why haven't the other two characters been affected? We don't know that they haven't. We don't know enough about them yet, but it's likely to surmise any of the following regarding time traveler actions conducted in the past:
- these actions haven't affected their lives at all
- these actions haven't affected their lives significantly to notice
- these actions have affected them, but they either don't realize it, or don't want to let on about it yet, or are deliberately avoiding their personal lives
- these actions have affected them, and we haven't yet seen it revealed
This would be consistent with the machinations of the show's time travel processes.
Do note that the book the antagonist time travelers are using is written by the protagonist time traveler (Lucy Preston) and may be significant to her own history and not those of her companions; therefore they may only be affecting her. Alternately, since her companions were selected prior to her joining the team, it is possible the protagonist's companions originate from a prior timeline that no longer exists, and we have yet to have this revealed.
Also, based on the aforementioned time travel rules, the mere existence of this book is key that the Lucy we are observing originates from a timeline where a Lucy from a different timeline got trapped in the past and never traveled back to her "New Present". That Lucy, and not necessarily our observed Lucy, wrote the book. The fact that there are two time machines in play, also complicates the situation, especially if it adheres to "Primer" rules, which is a whole other digression.