do I edit the StackSizeController.json or StackSizeController_vanilla-default.json in the data folder, I edited the StackSizeController_vanilla-default.json file with unlimited size but if I reboot or update the server it reverts back to the default size

Leave the Stacksize vanilla folder in its original state,
You can adjust amounts in the StackSizeController CONFIG json file
This is mine

{
  "RevertStackSizesToVanillaOnUnload": false,
  "AllowStackingItemsWithDurability": true,
  "PreventStackingDifferentSkins": false,
  "HidePrefixWithPluginNameInMessages": false,
  "DisableDupeFixAndLeaveWeaponMagsAlone": true,
  "GlobalStackMultiplier": 1.0,
  "CategoryStackMultipliers": {
    "Weapon": 100.0,
    "Construction": 200.0,
    "Items": 1000.0,
    "Resources": 600000.0,
    "Attire": 100.0,
    "Tool": 500.0,
    "Medical": 500.0,
    "Food": 2000.0,
    "Ammunition": 1000.0,
    "Traps": 500.0,
    "Misc": 1000.0,
    "All": 1000.0,
    "Common": 100.0,
    "Component": 500.0,
    "Search": 10.0,
    "Favourite": 100.0,
    "Electrical": 50.0,
    "Fun": 1.0
  },
  "IndividualItemStackMultipliers": {},
  "CategoryStackHardLimits": {
    "Weapon": 50,
    "Construction": 200,
    "Items": 1000,
    "Resources": 600000,
    "Attire": 100,
    "Tool": 500,
    "Medical": 500,
    "Food": 2000,
    "Ammunition": 1000,
    "Traps": 500,
    "Misc": 500,
    "All": 100,
    "Common": 100,
    "Component": 500,
    "Search": 100,
    "Favourite": 100,
    "Electrical": 20,
    "Fun": 0
  },
  "IndividualItemStackHardLimits": {
    "electric.simplelight": 200,
    "flameturret": 50,
    "rocket.launcher": 20,
    "lmg.m249": 50,
    "rifle.lr300": 50,
    "rifle.l96": 50,
    "riot.helmet": 50,
    "jackhammer": 20,
    "multiplegrenadelauncher": 100,
    "flamethrower": 50,
    "rifle.bolt": 50
  },
  "VersionNumber": {
    "Major": 3,
    "Minor": 4,
    "Patch": 3
  }
}

​

And you make adjustments in the \oxide\data\StackSizeController.json
Here are a few examples. Just remember that the DATA file MUST be edited with the plugin UNLOADED

"ItemId": 174866732,
        "Shortname": "weapon.mod.8x.scope",
        "HasDurability": false,
        "VanillaStackSize": 1,
        "CustomStackSize": 50
      },
      {
        "ItemId": 952603248,
        "Shortname": "weapon.mod.flashlight",
        "HasDurability": false,
        "VanillaStackSize": 1,
        "CustomStackSize": 50
      },
      {
        "ItemId": 442289265,
        "Shortname": "weapon.mod.holosight",
        "HasDurability": false,
        "VanillaStackSize": 1,
        "CustomStackSize": 50
      },
      {
        "ItemId": -132516482,
        "Shortname": "weapon.mod.lasersight",
        "HasDurability": false,
        "VanillaStackSize": 1,
        "CustomStackSize": 50
      },

but I want unlimited stacking?

MechWarriorZero

but I want unlimited stacking?

Sorry cant help, good luck with it

its still reverting back to the default if I either update or restart my server, I like the old version of stack size it didnt have this issue, this need to change so it wont do this