Since support for IDML is coming, but not .indd, I looked into the possibility to export all my old .indd files to IDML. This is generally useful for future-proofing anyway, since I won't be able to run my old version of InDesign (CS5) forever. I'm happy to report that this script was really good, it did everything I was hoping for. There was some trial and error and some issues (I have to delete batch_convert.txt for every run) to get there but eventually I got it to search folders and subfolders for any .indd file and export it as IDML, and it worked.