The following steps are commands to run in a Terminal.app command prompt. The first step assumes that you have already changed directory with the cd command into the directory that contains the .ipa file (UnifiedSingleViewIphone1.ipa in this example.)
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Expand the
.ipaarchive:ditto -xk UnifiedSingleViewIphone1.ipa ./original
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Add back the symbolic link, overwriting the incorrect non-linked version of the file:
ln -fs ../.monotouch-64/UnifiedSingleViewIphone1.exe original/Payload/UnifiedSingleViewIphone1.app/.monotouch-32/UnifiedSingleViewIphone1.exe
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Re-archive the result into a new
.ipafile:ditto -ck original UnifiedSingleViewIphone1_new.ipa
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You can now upload
UnifiedSingleViewIphone1_new.ipato HockeyApp (or any other desired destination).