The attached file has a basic object rotated 90 degrees on the y axis (Z-up). If I use refinery to convert to Y-Up the matrix is changed incorrectly. The rotation is applied to the x-axis (it should be applied to the z-axis after the conversion).
Z-UP before running refinery axis covert
<matrix>0 0 -1 0 0 1 0 0 1 0 0 0 0 0 0 1</matrix>
Y-UP after refinery runs axis convert
<matrix>0 0 -1 0 -1 0 0 0 0 1 0 0 0 0 0 1</matrix>
object rotated 90 degrees on the y axis (with z-up)