It was used in 2016 as a symbol of protesting the US’s passing of PROMESA, a law making a board control parts of the island’s economy and having unpopular measures such as decreasing the minimum wage by three dollars. A group painted over a famous mural of the flag with black:

After this, it became used all over to protest budget cuts and the weakening of Puerto Rico’s autonomy. Part of a letter from the people who painted the door (emphasis mine):
The laws, the governors and the courts, up to this moment, have not served in the interests of the people. To replace these colors with black (the absence of light) creates new readings. Ours is a proposal of RESISTANCE, not to be thought of as pessimist. On the contrary, it speaks about the death of these powers just as we know them, but hope is still present in the white stripes that symbolize individual liberty and its capacity to claim and defend their rights.
May this act serve as an invitation to reflect and to take action upon the collapse of the educational and health systems, the privatization and destruction of our natural resources, our colonial status, the outrage against our future workforce, the payment of an illegitimate debt, the imposition of a non-democratic government, the strangulation of cultural efforts among other things. This act is the evidence that there’s an artistic community that is not willing to give up, that will stand up and fight against the impositions of an absolutist government and its policies of austerity; their most recent example: the Puerto Rico Oversight, Management, and Economic Stability Act (PROMESA).
The full letter (scroll down for English
Source: Mother Jones. Image source.