My recommendation would be to not attempt to merge the two datasets. Instead, perform cokriging. Cokriging will use information from both datasets to make predictions, but it won't assume that the two datasets have the same statistical properties. Even if the two datasets do have identical statistical properties (implying you can safely merge them), you won't lose much by performing cokriging compared to merging the datasets and performing univariate kriging. The only disadvantage is that you will have to estimate two semivariograms and one cross-covariance curve rather than just one semivariogram.
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