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Corrupted Alignment File or Something Else?

Today I encountered an unusual error within PC-DMIS, or at least one that's new to me- changing the X, Y, and particularly Z coordinates that are being shown in the probe readout.

We are using build plates with Tool-Lok, and today I was switching back and forth between two separate plates taking measurements. One plate is raised about 15 inches above ground level, while the other is built into the floor. On both plates, I would close the active file, move to the new plate, open the relevant file, and immediately run into problems. In one case, the TCAD readout was displaying the probed surface as being approximately 3/8ths of an inch further out than it actually was.

The most problematic, however, appears to be tied to the alignment file for one plate. At resting height, the arm reads a Z value of approximately 25 inches. However, upon opening the relevant file, that Z value suddenly changes to 7 inches. If I move the active line above the Align command in the program, Z values return to something close to normal- but for obvious reasons that's not really viable as a solution.

I've tried locking into the plate using a file associated with the second plate, and that works just fine- Z values are accurate to prior measurements. And just to make sure it isn't human error, I double-checked to be sure that I wasn't mixing up files.

I'm guessing that the alignment file has been corrupted somehow and needs to be rewritten in order to correct the problem, but I'm wary about having to do this repeatedly, and if this is a known issue with a best practice to avoid it, I'd like to know.

Anyone have any insight or experience with this sort of situation?