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Can I ask what you're using to do lycoris merges? Kohya only seems to support merging them into checkpoints, and SuperMerger just outright doesn't support them. Or are you merging into a checkpoint and then extracting that?
Kohya does it just fine, at least from the command line tool. Here's what a typical merge command might look like:
./venv/Scripts/python.exe "networks\svd_merge_lora.py" --save_precision float --precision float --save_to "C:\ai\automatic\models\lycoris\temp.safetensors" --models "C:\ai\automatic\models\lycoris\first_lyco_to_merge.safetensors" "C:\ai\automatic\models\kycoris\second_lyco_to_merge.safetensors" "C:\ai\automatic\models\lora\you_can_merge_loras_with_lycos.safetensors" --ratios 1 .7 .7 --new_rank "256" --new_conv_rank "256" --device cuda
Adding "--device cuda" makes it faster, but occasionally it errors out for some reason. When that happens, remove it from the command and run the merge on CPU, and it should work ok.