In Season 4 of The Flash The Thinker infects Gideon with a virus and she goes out of control.
What happens to her after that?
Certainly there is no reference to the Flash's Gideon in Season 5 so far (as of Ep.4) but there does seem to be confirmation that Gideon is still not available to the team.
In Season 5 Episode 1 Nora there is this refernce...
I'm sorry I was too late.
It took me a while to find where the Legends were. Well, when they were.
But we got their Gideon to scan Nora's blood sample.
Clearly if the Flash's Gideon was still available they wouldn't need to use the "future" Gideon for analysis.