When you use checkboxes and "Toggle enable/disable" action to enable selected steps, the system set Run this step option to "If no prior step failed", so conditions get redundant and cleared. I agree this is probably can be improved. Thanks for your feedback, I will forward it to the Product team for further review.
For the moment, please use the following workaround. Instead of using the "Toggle enable/disable" action, if you want to keep conditions, change "Run this step" from "Never" to "If condition satisfied" on each step you used conditions. In this case, the system won't clear the conditions.