I set my renown to zero for upgrades too, I also use SH3Commander and have no problem with the file being overwritten.
Just make sure that you rollback SH3Commander before you put in the changed Basic.cfg file.
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GWX 3, JSGME 2.3, Sh3 Commander 3.2 SH3 Gen 8.1, Water Stream for U-boats, LRT LITE 2.0, Lifeboats for SH3
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