Background color drops when exporting to InDesign

I have documents that I've used for years without a glitch... Now I go in to update it with text edits, and when I export the PDF the background color completely drops out. The background color is creating by filling an unassigned object with a custom CMYK swatch color. In some documents it's on a bottom layer, while on others everything is on one layer and this is just all the way at the bottom in object order—it doesn't seem to matter either way, neither will export. I have not redefined the [paper] swatch, which is the only troubleshooting suggestion I've found online after hours of searches. HELP! If I pull the edges of the colored object within the live area instead of all the way out to the bleed it will show up, but that is not a viable solution.