Since it took me forever to figure this out:

It is possible to do a network Hotsync under Linux (see TheIdealPersonalDigitalAssistant):

<example>
pilot-xfer -p net:<your_ip_address> -l
</example>

You then just have to run a network sync with =your_ip_address=, assuming that you got the network running.

Version used: pilot-link 0.11.7.