It can happen to you when working with different Partials, that some of them are gone if you re-open your RapidWeaver project. The reason for this is the architecture of Stacks Partials. If you want to get rid of a Partial, it must not be used somewhere on your project in RapidWeaver. If not used, a Partial will be deleted.

Build a separate page for your Partials

If you build some similar Partials and are not sure if you want to use them, place your Partials on a separate page in RapidWeaver. I add a page, set it as draft (it will not be published) and uncheck the "Show in navigation" checkbox. On this page I place all Partials I want to keep and not want them to be automatically deleted because not using them on a page. I often use this trick for building several Foundation Site Style Partials.