Sarah Abu Lebdeh, 27, and Ahmad Rashad Nadir, 28, sparked national condemnation when they were recorded saying they would refuse to treat Israelis and appeared to threaten violence towards them.
The pair made the alleged threats on an online video chat platform in February, while they were working a night shift at southwest Sydney's Bankstown-Lidcombe Hospital.
Charges were laid after Israeli influencer Max Veifer shared footage of his conversation with the two nurses.
Abu Lebdeh was charged with threatening violence to a group and using a carriage service to menace, harass or cause offence.
A third charge, of using a carriage service to threaten to kill, was withdrawn by prosecutors on Tuesday in Downing Centre Local Court.
Abu Lebdeh is yet to enter pleas to the remaining two charges, which will proceed with the Commonwealth Director of Public Prosecutions.
She is on bail under strict conditions, barring her from using social media or leaving the country.
Her former colleague Nadir was hospitalised after the video emerged. But he was charged in March with using a carriage service to menace, harass or cause offence and possession of a prohibited drug.
He pleaded not guilty to possessing morphine and will fight the charge at a hearing at Bankstown Local Court later this year.
Nadir is yet to enter pleas to the charge related to the video, which will proceed with the Commonwealth Director of Public Prosecutions.
He previously apologised through his lawyer Zemarai Khatiz for the comments in the video.
The legality of the video - allegedly captured without Nadir's consent - will be challenged, Mr Khatiz previously said.
Outside court, he said the matter would take "a long time" to resolve.
Both nurses remain on bail and were excused from attending court on Tuesday.
They will return to court in November.
They have been prohibited from working as nurses nationwide by Australia's health practitioner watchdog and their registrations have been suspended in NSW.
Their comments attracted widespread criticism - including from the prime minister and NSW premier - amid community concerns at the time about anti-Semitic acts in Sydney and Melbourne.
Many of the highest-profile incidents in Sydney have since been revealed to have been concocted by criminal networks with no clear ideological motivations.
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