As far as I know you shouldn't have any problems. Make the full install of SH1, then your patrol disks (That will bring you to 1.1, I believe), and finally add patch 1.3 and the 1.31. In any case, the official patch 1.3 was already able to update any version, from 1.0, directly to 1.3 so it will anyway overwrite all outdated files.
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One day I will return to sea ...
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