Generally, installing mods whilst in base is OK. Installing whilst mid-patrol is definately a no-no.
For reference, SH3Cmdr makes changes to SH3 each time it runs which is commensurate to installing mods (SH3Cmdr works around the "installing whilst mid-patrol problems"). So you can see that it's OK to do so.
However, some players do lose their careers. Most times though, they are easily "reassociated" by some file/folder manipulation (renaming the career folders and renaming them back). Personally, I've *never* had problems installing mid *career* and I am regularly throwing different mods in and out of SH3 in order to test compatibility with SH3Cmdr.
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