I'm not sure how helpful this might be for some of you if you have very specific stack sizes or configuration. In my set up we generally just have a stack limit of 10k for all items that don't hold any water. I don't take any responsibility for you losing your existing data or configs, you should be able to back them up on your own. This process didn't allow me to use backups of my existing configuration because the files were no longer correct. FOLLOW AT YOUR OWN RISK
Looking through the forum it looks like some people were having the same issue I was. After upgrading to the latest plugin and after server restart (plugin unload), the plugin was generating a Vanilla Defaults data file. There was no way to overwrite or switch back to your own config. No commands would allow you to change stack sizes after.
The fix for me that seems to have been working after 3-4 restarts was:
1. Delete all existing data of the existing StackSizeController plugin. Take backups of anything important, but the files you'll want to delete are the Actual StackSizeController.cs file in the oxide/plugins directory, any StackSizeController files in your oxide/config folder, and all of the StackSizeController files under oxide/data - including the StackSizeController_vanilla-defaults file. I delete them in that order so that the plugin doesn't regen any of the files before it has been unloaded.
2. Verify the plugin was unloaded and none of the files above were recreated. Add the latest version of the plugin into your oxide/plugins folder.
3. Once the plugin has loaded and generated the config and data files, open up the oxide/config/StackSizeController file. At the very top of the file, change the first line from true to false.
I'm not sure if that is new functionality, but it doesn't seem to be working correctly. When set to true, the plugin generates the vanilla-defaults file on unload(happens during restart), and for some reason won't load custom stack sizes or allow manually setting them after.
4. Set up your plugin again. I would test with something easy before setting a ton of manual stack sizes. You may be able to use an old config or data file, but my data had seemed to be corrupted/incorrect after the vanilla defaults file was generated. When looking through your oxide/data/StackSizeController backup, if every item has a custom "VanillaStackSize" value and "CustomStackSize" set to 0, trying to reuse that file may not work for you, at least it didn't for us. Those values seemed to have been overwritten. I have verified that just setting hard stack size limits in the config file works for my setup and I am currently not defining any specific items or multipliers. Oxide/config/StackSizeController for my setup has
5. "oxide.reload StackSizeController" in console to pull the new config and verify your item stacks. Test a server reboot to see if anything disappears.
Again, if you have some time or environment without any people on, I would test setting one or two stacks sizes manually after changing the config option and restart the server. Don't waste your time redoing all of your work until you can see that it is working. This may work with your previously backed up config files and would be worth testing, but mine didn't seem to have the correct values and would not work.
For anyone asking why the chat commands don't work, it looks like that functionality was removed and all stack sizes are now set with console commands. Please refer to the new plugin documentation for setting stack sizes. Hopefully this helps someone.