Answer: There are no herbicides registered as safe on Thyme but deadly to clover. Thyme is pretty resilient, though. You may be able to lift up a large clump at a time, pluck out the clover, then lay the thyme back down. You might also consider just digging the thyme out, dealing with the weeds, then replanting it. This would give you an excuse to divide the plants if you want some for another location.
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