Works great in the Overworld and in the Nether, doesn't work in the End: chests in the end cities do not refill.
Minecraft 1.19. Used mods:

fabric-api-0.55.3+1.19
cloth-api-4.0.65
cloth-config-7.0.72-fabric
chestrefill-1.1.0-fabric

No other mods, no datapacks.

Humm, mod isn't dimension specific, do you have any special rules set up for end loot tables? Are you sure chests weren't looted previously?

I checked on freshly created worlds so the chests were never looted. My config file:
{ "defaultProperties": { "randomize_loot_seed": true, "allow_reloot_without_permission": true, "max_refills": -1, "refill_non_empty": false, "min_wait_time": 15 }, "// Map to override above config for certain loot tables only.": "", "lootModifierMap": { "sample_mod:chests/custom_loot_table": { "randomize_loot_seed": true, "allow_reloot_without_permission": false, "max_refills": 5, "refill_non_empty": false, "min_wait_time": 14400 }, "//minecraft:chests/igloo_chest": { "randomize_loot_seed": true, "allow_reloot_without_permission": false, "max_refills": 5, "refill_non_empty": false, "min_wait_time": 14400 } } }

Works perfectly in Overworld and Nether.

Maybe this is a problem with name end_city_treasure?

Not sure what do you mean, but mod just checks the config for any overrides, it doesn't check loot table names by itself.

When I put a chest in the End (also in the Nether and Overworld) using the command:

setblock ~ ~ ~ minecraft:chest{ChestRefill: {RefillCounter: 0, SavedLootTable: "minecraft:chests/end_city_treasure", CustomValues: {AllowReloot: 1b, MaxRefills: -1, MinWaitTime: 15}}}

everything works, chest refills.
Maybe this is a problem with name end_city_treasure ?

You guessed very well what I meant :) Now I know, it doesn't check loot table names.
It looks as if the mod treats naturally generated chests in the End like regular chests placed by the player.
Do not be offended, I ask to be sure: have you checked your mod in the End on Minecraft 1.19 Fabric? Your chests refill?

Whoops, didn't mean to close it.

I'll check it on my end.

Confirmed, chests don't get refilled here as well. What's even more strange, if I pick up the block using ctrl+middle click (to get the block with nbt data) it does get refilled

Indeed, it's strange :) Probably Mojang broke something as usual. ;)
I'm sure you can handle this problem. It is an excellent mod and it would be a pity that it would not be fully operational.

And now the surprise: the mod works perfectly fine in MC version 1.19.1 :)
So that's Mojang's fault :)
It's an excellent mod, thank you for your work.

Best regards.

Huh, what, wasn't expecting that :P. Glad to see it resolved though :).