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Yes, you can remove elements by specifying a “User Defined Analysis Script” in the Analysis Case. With that option you have full control of the OpenSees analysis.
If you want to look at an example on how to control the analysis I suggest that you study Example 3: http://openseesnavigator.berkeley.edu/wp-content/uploads/2015/09/Example3.zip
This example does not remove elements, but it shows you how to use “User Defined Analysis Scripts” for both static and transient analyses.