It is understood that Vice Admiral Saiyan ordered the blacklist to end late last year, soon after taking command.
Khun Chutima said: ''I appreciate the commander's decision. It indicates his concern for a good relationship with us and the media in general.''
Khun Chutima had been turned away from events involving the National Council for Peace and Order and was told she was banned from the base.
Phuketwan editor Alan Morison said the decision to take down the photo was a positive step in restoring the good relationship that the news outlet enjoyed with the Navy before charges involving criminal defamation and the Computer Crimes Act were laid late in 2014.
The case is scheduled to be heard at Phuket Provincial Court on July 14, 15 and 16.
Morison, whose passport has been surrendered to the court, is visiting Australia to see his ailing 91-year-old father after being granted permission to travel by court officials.
He and Khun Chutima remain on bail of 100,000 baht each, provided by the Andaman Community Rights and Legal Aid Centre, based in Trang province. Other groups and organisations have also offered financial help.
Most of the legal costs of the case are being met by the London-based Media Legal Defence Initiative.
In Thailand, a group of more than 10 lawyers have teamed up to provide legal counsel. They include the Human Rights Lawyers' Association, iLaw and SR Law.