Using the internal flash memory of a Zaurus for a swap file is not a good idea. If the swap file becomes corrupted, it will most likely be because the flash memory burned out.
When the Zaurus is attached to a PC as a storage device, the Zaurus is basically interfacing with the PC through software called Samba. Samba is an open source project which replicates the functionality of Windows networking code. The name Samba is derived from the abbreviation for the protocol that Windows computers use to network with one another, SMB. When the Zaurus SL-5500 interfaces with a PC as a storage device, it seems to use a special user name and password to log into the Windows PC which identifies the Zaurus as a storage device. The Zaurus's other processes should continue to run.