Hi @itsjustbusiness ,
The Transpose Master plugin requires that the TPose mesh it creates be unchanged in topology or point order. For the best results with this plugin you want to be working with a multi-resolution mesh with a clean quad low poly base and multiple levels of subdivision. The plugin creates a a new tool from all the subtools merged at the lowest level of subdivision, the user performs their posing on that, and the changes are transferred back to the original tool at the highest levels of subdivision.
So in order to get to this point you need to first transition to a multi-resolution tool. If you do not already have multiple subdivision levels you can create them by ZRemeshing or retopologizing by other means a new low poly mesh from your existing high res mesh, subdividing that mesh sufficiently to hold the incoming detail, and projecting the detail from the original mesh onto the new via one of the various methods.
Now you should have a tool with a low poly base and multiple levels of subdivision. Ideally this should be performed for all subtools that will be posed by the operation.
Use Transpose Master to create a new merged version of that mesh, pose it at the lowest level of subdivision, then send the changes back to the original tool. While posing this mesh you cannot use any operation that changes the topology or point order. Please be sure to read the Transpose Master documentation carefully. It describes some functions in ZBrush that may change the point order.
If you have broken a TPose mesh by changing the topology, you have only broken the TPose Mesh and not the original tool. Your original un-posed tool still exists in the file. You can simply go back to it and create a new TPose mesh.
Any pose work performed on your TPose mesh is likely lost unless you you can undo any changes back to before you changed the topology.
Good luck!