What will happen to my existing panels if I reinstall the panels module?
You will lost your custom panel configuration. To prevent that you can export all your panels to code with features.

This is because modules should remove its own data on hook_uninstall.

Features provides a UI and API for taking different site building components from modules with exportables and bundling them together in a single feature module. A feature module is like any other Drupal module except that it declares its components (e.g. views, contexts, CCK fields, etc.) in its .info file so that it can be checked, updated, or reverted programmatically.


This way you will have a features module with all your panels configuration. 

This are the steps:


Install features module.
Go to admin/structure/features/create
Give a name to the feature module.
Select panels configuration
Download the feature.
Move this module to the features folder (site/all/modules/features).
Uninstall panels
Enable panels
Active the feature on admin/structure/features


There are also 'export' and 'import' tabs/links on the Panels UI and Pages UI but this is a manual process and can be slower than using features.