When I first installed this mod and loaded a preexisting save file, I was given a list of removed recipes. This included all stacking recipes from your own Deadlock Stacking for Vanilla mod, as well as all of the default Deadlock's Stacking Beltboxes mod recipes. Now, these recipes were REMOVED from the game - items still stack just fine in the Beltboxes. However, the items are no longer recognised in Flare Stack mod. I used to be able to burn stacked items, but I no longer can. In fact, Flare Stack burners can no longer burn any stacked items from any of the three mods.

Additionally, stacking recipes from Deadlock Stacking for Vanilla no longer display proper names, instead showing "Unknown Key." In their pop-up info, I'm also seeing the items listed as Base Mod > Deadlock Stacking for Bob's, even though these are items from Deadlock Stacking for Vanilla.

Finally, it looked like my icons for both Deadlock's Stacking Beltboxes stacks and Deadlock Stacking for Vanilla items changed when I installed Deadlock Stacking for Bob's. The icons are objectively better, mind you, so I like them. However, it tells me that the mods are doing something to each other.

Please give me a copy of the "pre-existing save" so I can sync the mods it was using.

Certainly. I've uploaded the save to Dropbox at the following link:

https://www.dropbox.com/s/138fhkey4jahghv/Solo%203.zip?dl=0

It is fairly heavily modded. One mod you won't be able to find is Compound Splitters. I'm using the 0.17 version of that with the settings file manually modified. It works just fine in 1.0, but it won't auto-download or update for you.

edit Just a quick note - this is the save I'm using NOW. I don't know that I have the previous save still, but the only difference should be your mod. I've not really gotten a lot more.

The "Flare Stack" mod is being processed before the "Deadlock" mods. In his mod he is not seeing the recipes created by Deadlock as such it does not create a burn off recipe.
8.009 Loading mod Flare Stack 2.2.8 (data-final-fixes.lua)
8.927 Loading mod DeadlockStackingForVanilla 1.1.0 (data-final-fixes.lua)
9.643 Loading mod DeadlockStackingForBobs 1.1.2 (data-final-fixes.lua)

You could unzip the Flare mod and change its info.json to this, forcing the mod to run after the deadlock mods.

{
    "name": "Flare Stack",
    "version": "2.2.8",
    "title": "Flare Stack",
    "author": "GotLag",
    "homepage": "https://forums.factorio.com/viewtopic.php?f=93&t=21586",
    "description": "Adds structures to dispose of unwanted items and fluids.",
    "factorio_version": "1.1",
    "dependencies": [
        "(?)DeadlockStackingForBobs",
        "(?)DeadlockStackingForVanilla"
    ]
}

Thank you kindly. Tried it and it works just fine :) I'm a version behind (still playing 1.0) so my Flare Stack version was 2.2.7, but that was an easy fix. Frankly, I'm somewhat embarrassed I didn't think of this myself. I suspected it might be something to do with mod order, but didn't know how to fix it. So setting up mod dependencies is the way to go? Cool, thank you :)

I wonder if this is worth bringing up to the Flare Stack mod maker. Deadlock's Stacking Beltboxes seem to be a fairly popular thing, after all.

His script runs at 'data-final-fixes.lua' I am working to change mine to run at 'data-update' so it might be OK

Seems too many things run in 'data-final-fixes.lua' for Bob/Angel/Seablock that I am going to have to move things back there.

I have asked "GotLag" to add the dependencies to his mod.