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I understand the problem and can give you a work-around. But, I don't have the solution and it is bugging me too. :-)
Robohelp is capturing your fully qualified path name rather than the relative path name. For example:
What is should be capturing is either the main or the subfolder directly to the left of the file name. Like...
The fully qualified name is correct for external sites such as http:\yahoo.com, but the relative path is needed to copy your help site or online book site to another location or server. (Including the ISSL! folder where you are looking at your output.
I have three projects running on Robo 5. Two do this correctly. In the most recent project, I am having to fix the link, change it to relative, for every internal link I make.
Does anyone know of a default setting somewhere that will fix this.
Meanwhile, you have a work-around that will keep you going and maybe help keep your sanity.
We have a 40-project merged WebHelp system, with huge amounts of cross-project linking,
If RH "sees" the project/topic close by, it will usually create a relative path. If it does not, it has to guess (which will usually be wrong). That is, before I create links to project 32 from project 4, I make sure to copy project 32 to my local machine in the same hierarchical structure it will have in the output (source projects 1-40 under the /projects folder and output projects 1-40 under /mergedProjects folder).
REMEMBER: Your links must reflect the relative path to other topics no matter where the help gets copied to after publishing!
Linking to topics several folders away, or on different drives, will always result in absolute links that you'll have to fix.