The mod to the camera changes the distance for the auto focus sensor.
The only way of retaining the auto focus function is to either re-set the position of the sensor or replace the removed filter with a clear or UV-IR filter.
To use standard EF lenses with a mod you need at least a clip in filter to reach focus. Adding a clip in filter allows you to manually focus using the Liveview or viewfinder.
HTH
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