Overview
You are using, for example, Infeed + Reject and you want to change to, for example, Infeed + Outfeed.
Note :
1) stop any run before changing the Counter in the Production Mode
2) un check the Equipment in the Material Manager
3) change the Counters (enable/disable/delete whichever works for you)
4) restart the Production Module 
5) re assign the Material(s) and make sure the correct Count Equipment are selected

Applies To and Version Info
2.0 / 3.0 (Analysis code logic)
Details
Production Model Counter Tab
for Infeed + Reject

for Infeed + Outfeed (note Reject is not enabled)

Screenshots
Running with Infeed + Reject showing in Analysis

Running with Infeed + Outfeed showing in Analysis with Time Frame that includes the Run with Infeed + Reject

Explanation
Unfortunately the Historical Analysis will not show a break down between the different runs
This is working as designed
If the line has Reject Counters, use them (Infeed + Reject). Else calculate Reject (Infeed + Outfeed).
We look for any Reject Counters on the line or any cells at the time the Analysis is run.
If at the time Analysis is run there are no Reject, we will calculate Reject based on Infeed - Outfeed.
References
Impact of Renaming a Counter
Keywords
Use the following keywords as labels. Remove the words which are not associated with this article.
OEE
Configuration, Scheduling, Run-control-and-Monitoring: Adjusting-OEE-Run-values or Adjusting-Production-count, Analysis-and-reports, Production-data.