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According to iO9, the star of Arrow Stephen Amell was asked if the "Flashpoint" storyline would affect events of Arrow. Amell responded positively, but there is doubt of whether or not Amell even knows what Flashpoint even is. The report says that Stephen said "sure", but then said that he should have "I have no idea whatsoever". Considering that The Flash and Arrow take place in the same connected universe, it is possible that Amell doesn't know the big plan for this.
In the comic book storyline of Flashpoint, the story is about Barry Allen waking up finding out that he has no powers and that his mother Nora is still alive. He also discovers that the Justice League and Superman do not exist. It was quite an event for DC's comics, and it features very wild things like Bruce Wayne's father Thomas Wayne becoming the Batman and an Atlantis/Amazon war. It has even been adapted to an animated movie, which are known for being pretty accurate to their comic book inspirations.
Granted, the Justice League doesn't exist in the Arrow-verse as yet, however, the thing about time travel is that it is easy to go back in time and change things. This completely messes up the timeline, as is demonstrated on DC's Legends of Tomorrow.
However, this is the advantage of introducing time travel in comic book plotlines. It leaves the option of changing plotlines when they become old, or giving an opportunity of introducing new ones. For example, one thing that has happened recently is that CBS cancelled the show Supergirl and it will appear on the CW. Considering that The Flash and Supergirl had a crossover that involved a lot of crossing dimensions, this Flashpoint could be a way to bring Supergirl into the Arrow-verse continuity.
According to Screen Rant, Season 3 of The Flash is going to be "very different". This comes from co-star Carlos Valdes, who plays Cisco Ramon, and the first episode of Season 3 is going be called "Flashpoint". The Flash Season 3 will be happening in October on CW, but there isn't a specific release date.
