Make stereo files.
They're easier to handle and edit. Also there's less chance that the channels get out of phase during playback.
The last time I transferred samples from an audioCD to a HDD library i simply recorded the whole CD to two tracks in PT. Then it was easy to create and name a region for each sample (bd01.L, bd01.R etc). When that's done I just selected all and exported the regions as 16 bit stereo files.
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