Gary Haggarty, 44, is no longer to be prosecuted for three alleged offences.
His lawyers said these relate to possessing explosives and firearms.
His legal team are also set to challenge the "propriety" of prosecuting a man they say worked as a state agent for some of the remaining 209 counts against him.
On Wednesday, Belfast Magistrates' Court was told that a hearing to decide if the suspected UVF commander-turned police informer has a case to answer is scheduled for November.
Mr Haggarty has been waiting to discover if he will stand trial since signing an agreement to become an assisting offender under the terms of the Serious Organised Crime and Police Act (SOCPA) back in 2010.
The north Belfast man was charged with 212 charges covering a 16-year period between 1991 and 2007.
The prosecution case against him runs to 12,000 pages, with his alleged offences including:
Mr Haggarty, whose address is listed as c/o the Police Service of Northern Ireland, is believed to be living at a secret location in England.
He was not present for the latest stage in an ongoing court review of the case.
Outside court, Mr Haggarty's solicitor said a challenge would be mounted against some of the remaining charges.
"The defence forwarded written submissions to the PPS on 4 May dealing firstly with charges where we say the papers do not disclose a prima facie case, but also charges where there are issues in relation to the propriety of the charges at a time when the defendant was a state agent from 1993-2004," he said.
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Some charges against a so-called loyalist supergrass accused of a catalogue of murders and paramilitary crimes are to be dropped.