Checking "Apply DSP" upon handheld conversion and selecting Volume Leveling works great. However, if you deselect Apply DSP, the selected options in DSP studio (such as volume leveling) are still applied to the audio even though the option is greyed out; however, the original ReplayGain tag will remain, meaning the songs will be much quieter than their non-converted counterparts.
I confirmed by loading the converted songs into foobar2000 and running a replaygain analysis on them: all of the files that had been converted with the "Apply DSP" option unchecked showed replaygain analysis of 0.00, although they were still tagged with -9.32, etc original replaygain values.
Edit: I just tried rerunning sync with the DSP settings unchecked in DSP studio and the Replaygain is still incorrecrtly applied. I've deleted the cache, but the synced files (all the converted FLACs to MP3s) have volume levelling applied, according to foobar2000. The replaygain tag contains the original values calculated for the original FLAC file.