How can one delete a line in a stream? I do not see anything resembling a stream.DeleteLine method.

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There is no such method, but you can copy any number of characters between streams.

What do you want to get by deleting stream lines?

I want to utilize the  $$$AssertFilesSame macro to compare 2 files . The only difference between them are 2 lines that are allowed to be different. I wanted to open the file streams, go to those line numbers and delete them. Then run the $$$AssertFilesSame.  

It calls IsFileSame method from %UnitTest.TestCase class, which has a following  signature:

ClassMethod IsFileSame(file1, file2, ByRef diff) As %Boolean

Diff would contain differences between files. You can check that.

Thanks,  but the two different lines contain date and time stamp related information so the contents of diff would be unknown