When you say "most" of the hyperlinks have disappeared, do you mean that some
are still visible, or have _all_ of them disappeared? And when you click to
follow the links, do they reappear? If they've all disappeared, but reappear
when you follow them, then the character style named Hyperlink has been changed
from its usual blue with underline to white (if the space is still there but
empty) or Hidden (if the text around them has collapsed). Try modifying the
style back to its original definition.
If some are still visible, then direct formatting has been applied to the ones
that aren't -- again, either white font or Hidden. Select one and press
Ctrl+spacebar to remove all direct and character-style formatting, and then
assign Hyperlink style to it.