To reset the Live Datamart Server runtime environment, while the server is stopped we delete the generated folders lv-bin, lv-profile, and lv-systemdata. This also deletes all our alerts. How can we preserve alerts while performing this reset?

The lv-systemdata folder contains configured alert settings.

Keep the lv-systemdata/ folder and do not delete it when doing this. It has the LiveView.h2.db which is where alerts and other web-configured runtime settings are stored. No problems have been associated with leaving this folder from run to run. You may see what is in your LiveView.h2.db using the sb-cep/7.x/bin/lv-db utility. From the terminal in the LiveView project directory, use this command to emit the LiveView.h2.db as text to the console:
  $ lv-db -p . -e

We recommend only deleting lv-bin/ only if startup problems are observed and then as a precaution if there were .lvconf and .sbconf file changes since the last successful run. Otherwise leaving lv-bin after a known successful run and clean shutdown is a time-saver upon startup since this is where cached compilation results are stored.

The lv-profile/ directory is where runtime logs are stored. Removing it has no runtime impact, but its contents are useful for root-cause analysis if there is a runtime error in a prior session.