You can manually delete them outside SHIII.
taking vanilla SH3 as an example:
Go to My Documents\SH3\cfgcareers\kaleun name\
under there you will find a series of folders called 0, 1, 2, 3 etc. Each one for each patrol (starting at 0). The files inside this folder are the save game files. Just delete them. When you restart SHIII, the save game has gone and the others are still there.
if using MultiSH3 the folders will have names other than SH3, they will have names such as GWX, NYGM etc.
obviously 'kaleun name' is you career name.
p.s. make sure your in port first!
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