May I suggest the following workflow to you:
1) Rearrange samples through the Cleanup dialog, to get rid of any empty sample slots (http://wiki.openmpt.org/Manual:_Cleanup_Manager)
2) Shift+Click the Save button in the sample editor dialog to dump all samples. Move the "%sample_number%" to the beginning of the filename so that samples can sorted easily.
3) Edit your samples in an external application
4) Remove all samples, again through the Cleanup dialog
5) Load all samples into the sample editor again. They should be sorted automatically by the Operating System if you made use of the %sample_number% as described in step 2.

That should pretty much do what you want?

PS: Your samples don't magically become better by upsampling them. It's still the same old sample with missing high frequency content.

Thanks a million, I will give that a try! Hopefully it works but I am ending up with 100s by now, with each octave of each instrument having its own sample, with many dozens of instruments. I'm hoping your advice won't break how they are organised in the instruments or muddle the filenames too much.

As for the quality, they are originally much higher than 16bit@44KHz and actually get saved at a lower quality for lower-end systems, right down to being able to compose on a handheld. :P

Okay, I think step might be problematic, since it will also remove any references to these samples in the patterns/instruments... however, since the current OpenMPT builds already have some new on-disk sample functionality, I can probably extend this functionality to allow reloading all samples at once.

Please have a look at the latest test versions (r4606 or newer from http://buildbot.openmpt.org/builds/). The scenario I described earlier show now work with a few steps changed slightly:
1) Shift+Click the Save button in the sample editor dialog to dump all samples.
2) Edit your samples in an external application
3) In the tree view, right-click a sample and choose "Reload All".

Sorry for the delay, I've been sick over the last few days...

Maybe I'm blind but I can't find any "Reload All" button. I can dump all the samples just fine with good (although limited to 26 character?) filenames, but I can't bring them back in in an easy way. If there's a sample already there, I can see a 'Reload' item, but no 'Reload All'.

...On a side note, for some reason the main file buttons in the 'Samples tab' (top-left) are hidden under their own GUI, I can see half the 'save' button but the others to the right are hidden:-
http://www.violationentertainment.com/temp/openmpt.gif

The file name length itself shouldn't be limited, but yes, sample names are limited to 25 or something characters in IT/MPTM.
Did you maybe right-click on a sample that doesn't have a sample path set? That's the only possible explanation that I can see right now for "Reload All" not showing up.

Regarding that screenshot, it looks to me like your custom Windows theme messes up with icons sizes and makes them larger than OpenMPT gives them space. Surely OpenMPT won't be the only application where things are larger than normal because of this theme?

Okay, forget the theme issue, you are right. :P

I got it to work by following your instruction of setting the path. I only needed to set the path for 1 sample and then I can see "Reload All" menu item suddenly and it works for all samples. I didn't even need to do a cleanup.

I've only done a very quick test so far because I need to organise all of my samples, but as best I can tell - this is working! :D Very happy and thank you!

Oh yes, you're right - Reload All only shows up when Reload would be shown as well, i.e. if the selected sample is a linked sample. This is probably not the smartest thing to do...

Reload All should now always be shown if at least one sample has a path set. I'll consider this fixed/implemented then. :)