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Is it possible to distinguish multiple patterns when designating exclude/include filters? Say for example I want to ignore *.exe and *.dll when comparing directories. Is it possible to set that up as a pattern?

I am familiar with regular expressions and tried *.exe|*.dll but that didn't seem to work.

Yes. These are not regular expressions; they are comma-separated (as the name states at the top of Options | Dir Comparison ("Name filters (comma-separated patterns)") DOS-style patterns. So in your case you'd use

*.exe,*.dll

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