Presumably you or your mother has already asked Immigration Bureau, and from the Bureau has heard about your grandfather's [koseki-touhon].
: she wanted to change it to have a longer visa by using her nikeijin status.
: Do you think it is possible that she can process her visa there coz some people are saying that she coul'nt and that she needs to go back here in the philippines?
Visa is one thing, Status of residence is another thing.
But.... To change legal Status of residence for a longer-term residence, there may well be cases where a foreign national has to leave Japan and apply for a visa which corresponds to the legal Status allowing the longer-term residence.
I think Immigration Bureau will judge whether your mother has to do so in this case.
The fact that your grate-grandfather and grandfather were Japanese nationals doesn't bring you the legal Status of residence which your mother is now hoping to acquire.
This legal Status is not naturally given to a Japanese national's grandchildren or their descendants.
: Is it true that the japanese government made a law that all nikkeijin papers should be process by an authorized foundations?
If your mother is a Nikkei person born around 1945 or before, then maybe her visa application could be directly accepted by a Japan's diplomatic establishment in the Philippines.
Laws consist of Acts which passed the Diet (after lawmakers' discussions) and rules based on Act(s) which were put by the government or governmental authorities.
Immigration Control and Refugee Recognition Act itself does not state clearly that a [koseki-touhon] is required in such a case as your mother's.
Anyway, a Japanese parent's [koseki-touhon] is considered to be the best one to prove that your mother was born as a child of a Japanese national.
If your mother, for example, belonged to a Japanese school while she was a Japanese national, maybe the school's record, if any, could prove that.
However, if no one (still alive) knows about her days as a Japanese in Japan, or if she has never been in Japan while she was a Japanese, then it's not easy to find a clue on Japan side to locate the place more minutely than Fukui, Japan, I think.