By Fiddler traces I suppose that you mean Fiddler's Session Archive Zip (SAZ) files. If this is the case, please note that these files are simply zip files that are constructed in a particular way that Fiddler understands. You could rename the .SAZ file to .ZIP and use the Windows Explorer to see what is the inner structure of the SAZ archive. Basically, for each session x there are 3 files in the "raw" directory of the archive: x_c.txt, x_s.txt and x_m.xml, where x is the id of the session. x_c.txt is the client request, x_s.txt is the server response and x_m.xml is some metadata about session x.
You could write a script or a small program, which opens the archive for modification, iterates through all x_c.txt and x_s.txt files and replaces all lines in the headers part which begin with ^(Set-)?Cookie: MSIS(\w*)=(\.)*$ with just ^\1Cookie: MSIS\2=
I hope that this information is helpful to you.
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