The use of the singular it seems inappropriate as the pronominal referent for the preceding plural “all things”; thus Joseph Smith edited the it to the plural them. Semantically, “all things” is equivalent to ‘anything’—that is, Nephi is saying that he can do whatever God commands him. In verses 50–51, Nephi gives two specific examples, one theoretical and one actual: changing water into earth and receiving instructions from the Lord on how to build a ship. There is no implication that God would literally command Nephi to do “all things”—that is, everything. Thus the use of the singular it in the original text is actually appropriate, given the intended meaning. The difficulty in understanding comes from the phrase “all things” rather than from the singular pronoun it.
There is one other example where “all things” is used in a context such that the appropriate pronominal reference is the singular it, thus showing that this kind of usage is not accidental:
Unlike the example in 1 Nephi 17:50, the it in Ether 3:26 has not been edited to they.
Summary: Restore the singular pronoun it in 1 Nephi 17:50; the use here of “all things” means ‘anything’ and thus the singular it is semantically appropriate, just as it is in Ether 3:26.