I'm no longer seeing the completed check mark in the main window. Maybe the texture name changed or something?

Agreed, I'm seeing this as well. Was able to temporarily fix the Aiding the Accord: Time Rift tracker (#756) but once it's complete, there's no checkmark.

READY_CHECK_WAITING_TEXTURE and READY_CHECK_READY_TEXTURE are changed to atlas.

I messed around with trying to figure out how to use the atlas, but wasn't getting anywhere. For the meantime I made a simple mod to get the completed marks back.

Within Modules folder, modify Progress.lua and Core.lua.

Replace all instances of: "\124T" .. READY_CHECK_READY_TEXTURE .. ":0|t"

with: (GREEN_FONT_COLOR_CODE .. "X" .. FONT_COLOR_CODE_CLOSE)

This will give you a green "X" where we used to see the checkmarks.

I messed around with trying to figure out how to use the atlas, but wasn't getting anywhere. For the meantime I made a simple mod to get the completed marks back.

Within Modules folder, modify Progress.lua and Core.lua.

Replace all instances of: "\124T" .. READY_CHECK_READY_TEXTURE .. ":0|t"

with: (GREEN_FONT_COLOR_CODE .. "X" .. FONT_COLOR_CODE_CLOSE)

This will give you a green "X" where we used to see the checkmarks.

Can you tell me in detail how you fixed it?

Great fix, thanks @crusha015!

I took your idea and also did this for the ? textures:

Replace:
"(\124T" .. READY_CHECK_WAITING_TEXTURE .. ":0|t)"
and:
"\124T" .. READY_CHECK_WAITING_TEXTURE .. ":0|t"

with:
(RED_FONT_COLOR_CODE .. "?" .. FONT_COLOR_CODE_CLOSE)

Sorry, the Core.lua file is not within the Modules folder, but rather the SavedInstances/Core folder.

I created a pull request with my modifications. I think you can download the modified .lua files from the pull request:
#759

Original textures:

"\124T" .. READY_CHECK_READY_TEXTURE .. ":0|t"
"\124T"..READY_CHECK_READY_TEXTURE..":0|t"
->
"|TInterface\RaidFrame\ReadyCheck-Ready:0|t"

"\124T"..READY_CHECK_WAITING_TEXTURE..":0|t"
"\124T" .. READY_CHECK_WAITING_TEXTURE .. ":0|t"
"(\124T" .. READY_CHECK_WAITING_TEXTURE .. ":0|t)"
->
"|TInterface\RaidFrame\ReadyCheck-Waiting:0|t"

Sorry for delayed patch. Been a tough week and get fixes pushed at weekend.

Thank you LiangYuxuan for all your hard work, I didn't see them was posted when I posted mine so I will just wait!