You'll basically need to store the encoder count in a memory location. Then, on first scan, you can write the stored number back into the $encoder.acc location.
That's half right. The accumulator location is an output from the counter hardware, writing directly to it won't help. The workaround requires three registers...we'll call them Accumulator, LastAcc, AccOffset...and LastAcc and AccOffset must be retentive.
1. In $tFirstScan, MATH AccOffset = AccOffset + LastAcc
2. In $TopOfScan, MOVE $Ctr.Acc to LastAcc and MATH Accumulator = $Ctr.Acc + AccOffset
3. In your code, reference Accumulator instead of $Ctr.Acc
4. When you reset the counter, be sure to reset AccOffset
We will definitely fix this. The fix will be in the next release.