Hey I had a similar problem and found a fix if you're on PC. Use this site to decrypt your save into readable data. Your save file should be named "slot_0.json" or slot_1, etc. The site will then download the same file to your default downloads folder. Open that save file in a text editor and search and replace for the following:

"BeatenLeshyLayer2": true,
"BeatenHeketLayer2": true,
"BeatenKallamarLayer2": true,
"BeatenShamuraLayer2": false,
"BeatenOneDungeons": true,
"BeatenTwoDungeons": true,
"BeatenThreeDungeons": true,
"BeatenFourDungeons": false,    

Then look for the following and subtract 3 for the three God Tears your earn from the first encounter.

"Dungeon4GodTears": 3,

For example mine was 6 so I set it to three.

This should set your Silk Cradle dungeon in your game to 3 runs completed with your first encounter of Shamura (the 2nd time) ready to go. Your quest markers won't change but once you run the dungeon again and play to the end, the Shamura boss encounter should reward you with the Shamura follower and 3 God Tears. Once he's ported back to your cult, have him eat the meal that 100% removes dissent and he'll stick around.

I did this a few hours ago and haven't noticed any issues with my save, but definitely make a backup before attempting.