This can be a painful problem to deal with, namely because there are a large number of causes.
I’ve worked with some seriously intense files before and had to export them to Photoshop as part of my procedures at work. The main problem I’ve found is that Adobe’s products don’t always communicate as well as they should. Photoshop has its own way of dealing with layer effects for instance and not all Illustrator effects translate when exported.
Before you start:
I use the Document Info tool to get a detailed look at all the components of my file.
If you “unlock all” and “show all” of your objects and layers, then in the Document Info window, click on the little black arrow to bring up more options. You can then specify ‘Objects‘.
This will show you all of the information relating to all the objects in your file. You should be able to determine if there are any irregularities such as incorrect colours or open paths etc.
You will have to conduct an isolation test with your layers. Hide half of them and try to export. Then with the other half.
Whichever exported half creates flattened layers in the exported PSD therefore contains the culprit object.
Keep dividing the number of layers in Illustrator until you narrow it down to the one master layer, then repeat the process with the sublayers, groups and finally the individual paths, blends or meshes. Eventually you should find one or more objects causing the problem.
As far as I can tell, the data attributed to these objects has been corrupted at some point and needs to be refreshed/re-written.
In order to do this, you need to do one of the following:
Overprint Colour Fills:
If you find any overprint colour fills, change them to regular fills. Re-exporting should work fine now.
Only normal transparencies seem to export correctly. Most of the effects created with Illustrator’s newer features can be replicated easily manually or by other methods. If you intend to export your art to Photoshop, keep that in mind to avoid running into trouble.
Having too many blends or blends with too many subdivisions can create unnecessary file sizes.
Releasing a blend and then re-blending the 2 or more paths can sometimes fix the problem.
Alternatively, select all of your blends and double-click the blend tool in your main toolbar. This will bring up your blend options. Select ‘Specify Steps‘ and then give it a lower value. The smaller your blend, the less subdivisions you will need.
Corrupted Paths or Gradient Mesh:
If a path is corrupted, simply offset it by a value of O (Object > Path > Offset Path> O). This will clone the path exactly.
Then delete the original path/paths. It doesn’t matter what type of offset you choose. They will all yield the same result.
If the colours are not the same, the eyedropper tool should fix the problem (make sure you have Appearance ticked in the Eyedropper options menu).
If a Gradient Mesh is corrupted, simply refresh it by adding a random point along the outside path using the Add Anchor Point tool , or create a second co-ordinate point close to a pre-existing point using the Mesh tool .
Corrupted Group or Layer:
This is the easiest of the issues to resolve. Simple create a new Master Layer or Sublayer and drag the elements or groups over to the new layers.
Alternatively it could be the groups within the layers that are causing the problem. Simply release then regroup them again.