Default Substance Node Reference Not Found Upon Reopening Files

When I am opening a substance graphs that I have just worked on. A lot of the default build in node become ghost instance with error messages of "Reference resources not found". I have include images of the error messages.

When I compare the broken nodes with the correct node. The Graph instance value both nodes are very similar but have slight numbering difference. For example, the working Tile Sampler node have "pkg:///tile_sampler?dependency=1474624371" but the "ghost instance" Tile Sampler have Graph instance link of "pkg:///tile_sampler?dependency=1474432934"

On top of that, some working nodes have their input socket missing. which pretty much make the entire network unusable.

Any help is appreciated! Thanks!