Did they say what was set to overprint that should not have been?
No they did not just that I have many overprints. Not sure where to check.
1. Turn on menu View/Overprint preview and see what changes;
2. Window/Attributes, select objects and look at the panel if line/fill overprint is checked
3. Window/Effects: select objects and look for applied transparency or blend mode
Your printer should be a bit more helpful and give some more information. It could be they simply want a old fashioned PDF X/1a.
Removing overprint will change the printing (output) colors of objects. If what you want as output is the colors as viewed without overprint preview selected, then you can almost be sure that overprint colors can be removed.
In InDesign overprints are applied from Window > Output > Attributes panel. If you have not applied this deliberately to objects, it is most likely some object style settings caused this.
You can quickly remove all overprints in the document by Find-change:
1. Go to Edit > Find/change
2. Click Object tab and click "specify attributes to find" button
3. Select the checkboxes: "overprint fill" or "overprint stroke", whatever you want to remove, OK
4. Click "specify attributes to change" button
5. Keep the checkboxes of "overprint fill/stroke" unselected, OK
6. Make sure Search Document or All documents selected and click Change All
Thank you so much. Will do it and let you know.
Overprints can also be applied to text and tables, so you could also use find and change for text, but the object search will not get table fills and strokes
Also you have to worry about black text which usually should be set to overprint unless the point size is large (the default [Black] swatch can be set to overprint in Preferences). Large areas of black usually should knock out so it's best practice to create a new black or rich black swatch for large fills.