I'm afraid that there isn't a SQL Doc API that you can use, but it is possible to call a sequence of SQLdoc sessions by using a batch file calling the SQL Doc command line for each project.
You have to set up each project file first using the GUI, setting a target directory for each project, with source databases, passwords etc. The batch file can then call a CHM publisher through a command line to write CHM files using each target directory as a source. Simple root level html code would have to be written to call the 'index.html' from each target directory so that a tree structure would be displayed - however that would only have to be created once
The help file in SQL Doc under 'Using the Command Line' explains the command line syntax.