I have stopped using these small clay spots, just because the reasons you say; it´s not so easy to refill them. I usually build a large claypit (in the menu of bricks) right at the beginning.
The small holes can be filled but you need the same amount of clay to fill it as you got out of it; so making a new small spot to fill another is a “never-ending story”, as far as I remember you need a builder to fill it and it follows the limit of logs, so if you have more logs than the limit you´ve set, nothing will happen.
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