So, there's 2019 FitzSimmons, 2023 FitzSimmons who haven't time traveled to before 2019 yet (we'll call them "2023 FitzSimmons NT" for "no travel"), and 2023 FitzSimmons who are returning from the alternate timeline (we'll call them "2023 FitzSimmons R" for "returned").
What happens:
Enoch tells 2019 FitzSimmons they have to leave
2019 FitzSimmons go to Piper and Flint and ask for help
2023 FitzSimmons R arrive with the team
2019 FitzSimmons, Enoch, Flint, and Piper land the Zephyr
2019 FitzSimmons and Enoch go into space
2023 FitzSimmons NT return from having spent four years in space together (2019 FitzSimmons will become 2023 FitzSimmons NT)
2023 FitzSimmons NT go to Piper and Flint and ask them to protect the Containment Module, which contains Alya and 2023 Fitz NT
2023 FitzSimmons R (and the rest of the SHIELD team in hazmat suits) help 2023 Simmons NT retrieve the 2019 SHIELD team from the temple
2023 Simmons NT tells the 2019 team about the Chronicoms attacking them while the hazmat team, including 2023 FitzSimmons R
2023 Simmons NT and the 2019 team leave for 1931
The temple is destroyed and 2023 Fitz NT leaves for 1983
So, until the 2019 team left, there were three versions of FitzSimmons: 2019 FitzSimmons was in space preparing to study the Time Stream, 2023 FitzSimmons NT had just returned from studying the Time Stream were about to leave for 1931, and 2023 FitzSimmons R were helping the SHIELD team which had just returned to defeat the Chronicoms. So it was only for a short while, but there were briefly three versions of FitzSimmons existing simultaneously. After 2023 FitzSimmons NT leave (Simmons going to 1931 and Fitz going to 1983), there are two versions (2019 FitzSimmons and 2023 FitzSimmons R) until 2023, when 2019 FitzSimmons return to 2019.
I hope this helped, I tried to make it as not confusing as possible.