I now operate about 1000 100MB zips across 6 platforms of sampler and computer and have never lost any data once a disk was formatted correctly on the machine you're going to use for the storage/retrieval cycle, and tested before critical use.
I don't have experience of Akai (I know 5000 works well obviously, as does Kurzweil, they both use a PC format more or less) Emu or Roland with PC , but a thorough test is always a good plan before committing to a system.
I would recommend writing on the plastic case what format you have used, and especially in the case of Akai S 1000 to 3000 how many partitions you decided on, that can really assist when hunting for that lost program.
Also the various sub-formats of Emu can be a pain, "save as EIII" being a good work-round for them, as most samplers can read that.
There is a limit to the number of files you can fit on a zip ( seems to be 100 files) that seems to be got round by making folders before you transfer files.