The group was protesting the Israel-Hamas war.
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Judge Brendan P. Conroy dismissed 32 of the 44 charges against 26 Bay Area activists known as the GG26, most of them counts of false imprisonment.
However, some federal conspiracy charges still remain.
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One defendant's case was dismissed entirely.
The judge also signaled openness to reducing felony charges against eight protesters to misdemeanors and could adjust restitution amounts at the next hearing on Dec. 6, authorities noted.
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"Today's decision is a huge win for our clients and the community at large," said Jeff Wozniak, an attorney representing the protestors facing felony charges. "The clients know their actions were just, taken to speak up for the thousands of Palestinians murdered in the past year and that the initial, overly-harsh charges were merely an effort to silence their activism."
KGO-TV staff contributed to this report