Update your game
Iteration is the whole point of prototyping, and updating a Runner game is deliberately boring: edit in the browser, export again, install the new version. Your edits save automatically as you work, so the editor always reflects the latest state of the design. When you are ready to test the changes, run a fresh export and the new build replaces the old one.
For Local Play, the loop is edit, export, and reinstall with the Tabletop Deployer. The whole cycle takes a couple of minutes, which is fast enough to fix a broken deal rule between playtest games on the same evening. Card content changes are even quicker when your cards come from a Card List: update the spreadsheet, re-import the CSV, export.
Between sessions, batch your changes. Playtesting works best when you can attribute a difference in play to a specific change, so resist the urge to rewrite five systems at once. Change the one or two things the last session flagged, re-export, and test again. Runner makes exports cheap precisely so your versions can be small and frequent.
Keep notes on what changed in each version, even just a dated line or two. When a playtester says "this felt better than last time," you want to know which change deserves the credit. A design that improves through many small, tracked versions is the normal path from rough idea to finished game.