The fixed depth is added during the final phase of the conversion (when the PNGs with the stereoscopic bitmaps are written to disc). The fixed depth is not taken into account when BD3D2MK3D writes the <depth> tags in the temp 2D XML file. (That allows you to convert the temp XML file again with another fixed depth if you think that the resulting final depths are not good, without affecting the original depths extracted from the 3D-planes and already written in the XML.)
It is never necessary to redo the whole process if you need to fine tune the 3D subtitles. You can convert them again with the Tools menu, and overwrite the original 3D subtitle file. Then use the _MUX_3D.cmd to remux the final MKV with the modified subtitles. (Of course, in case of hardcoded subtitles, you'll have to restart _ENCODE.cmd, and that's much longer.)
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