When political independence was granted by the United States government, these occupied lands then came under the administration of the Philippine government. Evidence that these lands are now under the patrimony of the Philippines were its inclusion in the definition of Philippine territory, and visible signs of these lands being under the administration of the government, such as it being under the protection of the State's security forces and obedience of the people to the laws of the land.
Residents became and considered themselves "Filipino citizens". These include Bangsamoros who militated against the government. Bangsamoros consider themselves Filipino Muslims.
When organized militancy became visible, a huge segment of the Bangsamoros consider themselves not as Filipinos, but as "Bangsamoros" only and others, "Muslims" only. In the Noble Qu'ran, there really is no other nationality except the faithful as a "Muslim". Affixing another nationality in the term "Muslim" is considered shirk, since every one who professes to believe in Islam falls under the Nation of Islam, which is one nation under Allah SWT. The two billion Muslims around the world are citizens of the Ummah or Jemaah Islamiyah or the Islamic community.
In Mindanao, there are those who believe in this, which considers themselves only as "Muslims" and those who consider themselves as "Filipino Muslims". Some do not agree on being called "Filipino Muslims", since the term "Filipino" is rather an append to slavery.
Anyway, for Muslims, their religion is the top-most in mind, with citizenship falling second, even last of their considerations or priorities.
However, when property claims are being discussed, Muslims take these things very seriously. The struggle for property ownership is something very important for any Muslim. Fact is, the struggle for one's property is a cause or reason for jihad or a declaration of Holy War.
The believers are those who believe in Allah and His Messenger, then do not doubt [the verity of Islam], and jahadu (do jihad) with their properties and selves in the way of Allah; those are the truthful (49.15).
What the Sultan of Sulu is doing falls under his own belief that occupying his own property is his jihad. Those who follow him, is also following the righteous path because it is encouraged by the Noble Qu'ran and the Al-Muslim to help fellow Muslims in their strivings. Threats against property, life or one's honor are drivers for jihad.
The only question is---will this be a peaceful or an armed jihad?
Had the occupiers of Sabah been non-Muslims or even Muslim, the prescription is still a peaceful jihad. Muslims are encouraged to resolve these things in a peaceful manner, since the very act of negotiating peace is, by itself, jihad.
Now, whether or not these Muslims under the Sultan of Sulu consider themselves merely as Muslims and therefore, under the tutelage of the Sultan or as citizens of the Philippines, the fact remains that they are under the political jurisdiction of the Philippines and therefore, enjoys the rights of a Filipino citizen.
Being so, and respecting the rights of the Sultan of Sulu in his claims of ownership of Sabah, here comes the tricky part---how to resolve the impasse?
The best way is for the Philippine government to resolve the issue by silently backing the Sabah claim and creating an open channel between the Sultan of Sulu and the Malaysian government. This dispute, honestly, is between the Sultan of Sulu (the Philippine government in its back) and the Malaysian government which occupies Sabah as a lessee. Talks should be encouraged between the two.
I believe that this issue could be resolved peacefully if the Malaysian government agrees to raise the lease payments from its present state to, at least US$ 3 billion. I think the Sultan of Sulu will agree on this, since the only reason why it is occupying Sabah right now is it wants to publicly announce that Sabah still falls under the territories of the Sultanate.
Or, include the Sultanate of Sulu in the Federation of Malaysia, thereupon creating the concept of duality in citizenship for those who profess to follow the Sultan. A peaceful resolution is in the horizon. All camps should only reason and open their minds and adhere to the truth and mete justice to those who need it.