I think what's happening is that you are altering track parameters by using the SD card on your pc, and then the project info that is written by your R16 while the project is active is then not correct. When a project is open in your R16 it saves other data besides the audio. For instance, effect info, slider ride positions and so on.
Your approach needs to be, A record your tracks on your R16, B insert a USB stick into the Zoom's orifice and via the USB menu save either tracks one at a time or whole project to the USB flash drive.
C, work on your PC with the tracks, via the USB stick, saving any changes to that location.
D, plug your USB stick back in the R16 and select via USB menu file load, and load tracks into project (having aleady altered their file names in audacity by adding 1 on the end or similar or naming them, Vocal, Bass, Drums ect) just so you preserve the originals within the project.
E, load the tracks into your project, one at a time. F, push the button which is named "track" and select the new tracks you have loaded to the R16, one by one into the track positions you want, ensuring that you stereo link tracks which are going to have stereo files loaded into them.
You can then play around mixing your whole track using the R16 controls and the Job's a good un.
Obviously you don't trim anything from the starts of the tracks in audacity or you'll have some additional entertainment, but eq, compression and the whole array of other stuff available by using audacity can be used. it can be useful to have a couple of versions of some recordings which differ tonally after being manipulated in audacity which gives you the option to mix them on your Zoom to get another set of options sound-wise, when mixing your whole track, also useful for fattening up vocals by panning two tracks 10-20% left and right of center. Any additional duplicates must have different file names as already mentioned i.e drums1, drums2, drums3.
You can also mix some tracks together in audacity to free up tracks on your Zoom if need be, but be prepared to do that a few times as the requirements for those takes might differ slightly once you have all the animals in the zoo. There is no substitute for having full control of each individual take but if you do run out of tracks, master record a couple of takes on your Zoom and load that mix to one stereo track to free up a track. you can always re load the takes back into two tracks on the Zoom if you want to tinker again. You can even open a new project and load some of the same tracks and play around using two projects and then mix it all down in stages. Use what you have lol.
The same applies to any take that's a bit thin or you want to strengthen its presence in the overall track. Copy everything is a good start, and never mess with the SD card straight out of the Zoom other than copying from it. Exception being, using it on someone else's Zoom to save a copy of their project or tracks.
If you do, double up a number of takes to give you additional creative control, bear in mind that you'll need to drop the level of every track if you end up with a lot of tracks contributing to the whole. The reason being that you'll start clipping, as lots of quiet tracks can become very peaky when combined and soon max out your headroom.
all the best
Tim
