You can delete anything prior to your last save with no effect on the game as long as you keep the file called 'career.cfg' (it's the only file in your savegames folder with a unique name). It's that file that keeps track of all of your patrols - open it up with notepad and it'll give you all the information you need. I believe it's also this file that SH3 Cmmander reads for the realistic ship information.
I run over 15 careers to help me with testing new mods (two for each year plus a few 'play' careers) and when I want to clean up I keep the last three savegames and delete the rest.
I recommend you back up before messing with the careers folder... just in case!
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