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Hi jaybird135 and welcome to the RH community.
It sounds like you have zipped the OUTPUT from your webhelp projects. Am I right? If so, these files are very different to the SOURCE files. The output contains all manner of files (some with the same name regardless of the project) so it is best to keep the output separate.
Why? I regularly zip up both source and output. The structure takes keeps them apart.
This sounds more like JayBird is selecting files in the right hand side of Explorer and zipping them, then doing the same with another project.
The trick is to select a folder on the left in Explorer and zip that, then when you add the next project to the same zip file, make sure the two folders have different names, then WinZip should be OK.
That said, I think it better to have one project, source and output, per zip file.