I am guessing that you're killing off the character when train saver is enabled and restore it when it disables?
In any case there is an issue in that with an increased inventory size (due to armor bonuses) when train saver disables using anything other than the hotkey for starting it you get a bunch of messages about not being able to insert stuff due to inventory size and stuff just lands on the ground around you, rather than in your inventory.
This issue does not appear when you have enough space in your inventory (e.g. less than the default no armor stacks occupied), or when you use the Ctrl + T hotkey to stop trainsaver.
However when you hit Esc, or start moving when trainsaver is enabled, anything that exceeds default inventory (no armor bonus) size is dumped. Additionally your armor is losing its charge.

It also appears that I may have lost some armor, which just disappeared into nothingness.

Thanks for the report, that's an interesting issue. Can you please send a list of any other mods you have enabled so I can try to replicate it?

Trainsaver does not modify your character or armor at all so I suspect that this issue is being caused by another mod, but I still have some questions:
While trainsaver is active, are there any logistic or construction bots delivering items to you?
Are any character modifying mods enabled? i.e. Jetpack, a character skin mod, bigger inventory mods, etc.
When items spill out onto the ground, are they items that were previously in your inventory before trainsaver started? Or were they delivered to your character while trainsaver was active?

I think most other questions I have at the moment could be answered by seeing what other mods are active. However, if you have a save file where you can reproduce the issue that would be even better!

Thank you! :)

I don't think the bots are delivering things while train saver is active. My Inventory is stagnant at that time and I wasn't crafting anything. Trainsaver just auto enabled after a few minutes as per its settings.
The items spilled were previously in the inventory. There aren't any items around me and as soon as trainsaver disables a bunch of items appear around me, my armor loses battery charge and then bots start flying to refill my now unfulfilled requests.
Other mods are mainly SE and QoL: https://pastebin.com/Jej3EjuF (That list is slightly out of date, running 1.1.69 of base atm, and except SE all the mods are latest available version).

This is a bit necro but I think I know the issue. Mega Bot Start gives a weird special MK4 armor with Krastorio (SE?). It changes into a MK2 if the mod is disabled for whatever reason or trainsaver does anything. As a work around unequip the armor, disable mega bot start, and reequip. Trainsaver should no longer have any issues with resizing armor.