This is just my take on how it would cause a worldline shift

Sern was manipulating a lot of events behind the scenes with the time machine to watch the labmembers, the cause of all of those manipulations, and the cause of Sern's control over the time machine was this d-mail. so if you delete the cause, the effect is also deleted. in other words, the past and the future were reconstructed and the worldline shifted to an alpha worldline where WW III happens, and Makise Kurisu's death is a convergence , and Sern's time-machine research is either non-existant anymore, or their research progress is significantly reduced, and Sern know nothing about the labomem's research on d-mails and time-travel.

Sorry for my bad english.

Here is a quick explanation.

First d-mail caught by echolon>SERN discovers and uses it for time travel research>SERN takes over in 2036>Suzuha travels to 2010 before 1975 to meet her father. but sets coordinates into radio building. So canceling Dr. Nakabachi's conference (Kurisu can't attend so she doesn't die)>[Events of Steins;Gate]>First D-Mail (no other D-Mials sent as they were all undone)deleted by Okabe>SERN doesn't have enough info to take over.>WW3 occurs>Suzuha travels to 1975 to retrieve IBM 5100 to prevent Y2K>Travels to 2000>Travels to 2010 (Coordinates set right)>Dr. Nakabachi's press conference occurs>Okabe gets metal upa>Kurisu dies by Okabe Rintaro from the future>Dr. Nakabachi steals papers (with metal upa inside)>Dr. Nakabachi deports to Russia>Metal Upa prevents papers getting burned>Russia now has working time travel info>US gets involved>[Events of Steins;Gate 0].

So it doesn't matter the contents of the first D-Mail just that it was sent and Suzuha canceled the conference by accident when she traveled to 2010 to see her father. But in the beta timeline she knows her father and doesn't travel to 2010 first instead goes to other periods and when she arrives at 2010 she sets the coordinates correctly so the conference occurs and Kurisu dies and her papers get sent to Russia, then WW3 happens.