Best thing to do is check the focusing at the film plane first. If that is OK then just a readjustment at the focus screen is needed and you are in business again.
It sounds like the screen was changed because the standard screen was a ground glass style, not a split image. That may be the cause of your missalignment. It's not a big deal to adjust either. If you had the older TLRs, it would be a different story, they didn't have replaceable screens and adjustment was done by subtracting or adding a shim under the lens.