We have multiple Indesign files that use overlapping font files.
For this to work and prevent conflicts, we would have to put each template in it's own folder with its own Document Fonts folder.
Is there anyway we can just tell indesign to look for the fonts in a specific folder etc?
Please don't use the scripting forum for questions that have nothing to do with scripting.
The operating system takes care of fonts. As far as I know you cannot do what you ask for in InDesign. Specifically the location of the font files are not changeable with scripting.
Using overlapping and conflicting fonts in different documents seems like a very messy thing which should be avoided.