Not sure if it's a bug, or simply the way vMix functions. Changes to offline inputs don't appear to be saved with presets - perhaps to avoid accidental changes to an input which can't be checked.

As a workaround, if you want to swap 8 calls in a multiview on the fly, I'd look into doing it with shortcuts.

I think - but it's just a guess - that vMix checks for offline inputs when saving presets and considers them as invalid sources, which is why they're not 'sticking' in your multiview inputs.

As you know, only the first 8 calls will be active when you open the preset. But if you change the order of your inputs, so that calls 9-16 appear before calls 1-8 and then save, calls 9-16 will be active the next time you open the preset, so you could set up your second multiview. But, my guess is that your multiview with calls 1-8 will then lose its sources...

Even deleting and appending new calls on the fly is a pain, to be honest. A multiview which references deleted calls will have all its layer sources unset, so when you append your new calls (even to the same input slots), you'll still have to reassign them to the multiview layers (faster with shortcuts, but still...). All in all, I'd still be tempted to save each preset with 8 calls and a multiview, and load presets on the fly, especially with 3 machines at your disposal.

I'm still thinking this is abnormal behaviour. When appending Callers out of another file, it also reverts the name I gave the input back to the caller ID after saving and reopening the file. this also happens randomly. Some of the names stay, some don't, It seems totaly random, but if the name sticks once it will always stay, if the name doesn't stick, it will always revert back to the call number after saving and reopening the preset. This happens on 2 different machines.
It somewhat matches the behaviour of layers not being saved, since the layer will also stick with some inputs, but not with others, but will always come back the same way after reopening the file.