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Thin set is not intended to be a leveling cpmpound although many people use it as such, myself included. It can be used to over 1" in thickness if applied in layers no thicker than 1/4" at a time, and allowed to completly dry between applications. In order to do this you need to add acrylic to the mix instead of water. Each layer will need to dry at least 24 hours.
Mind you now I do not recommend that you use thinset for anything over 3/8". There are self leveling mixes that are better suited to this type of application.
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Best regards; The Home Smithy