Linking between Clean HTML projects

[Colum]

Hi. We're looking into implementing multiple Flare projects for the same deliverable (some 1100 topics) that will all output Clean HTML targets that will be published to Salesforce. We're going to divide the topics up into major functionality areas, one in each project. So my question is, what is the best way to link to a topic in one project to another. Can we:
- Link to the file name of the relevant Flare topic
- Link to the file name in Salesforce

If linking to a Flare topic, how does link work once migrated to Salesforce? I'm guessing that as long as all the Flare project topic files are located in the same location, it should be OK as long as there's no file path - just the topic file name. If linking to a Salesforce file, we won't always know the file name if the topic is a new file and hasn't yet been published to Salesforce. So this option seems to be a non-starter.

All thoughts, wisdom, and other forms of wizardry are most welcome.