In addition to what's been said ... and an item that has not been mentioned yet ... when migrating a site (from 1.9.19 to 2.2.highest ->) one will retain users but the files contained in all courses are in 'legacy'. Courses in legacy file system don't behave like new courses with new file system. Once a course is in legacy, it's in legacy forever. The same thing will happen when restoring a 1.9.x course - no users and legacy file system. While it doesn't 'hurt' anything now, it might, in the future, when/if Moodle code no longer supports 'legacy'.
So your options are basically:
migrate a site upwards (the 'moodle march') - one retains users but has legacy file system. A 'moodle march' is best done via git 1.9.current -> 1.9.19+ -> 2.2.highest -> 2.3.highest -> 2.6.highest -> 2.7.highest -> 3.highest. Reason for the 'pit stops' ... to address major changes at that point. If broken, fix at that point,, before marching upwards the next step. Examples: changes to assignment mod and quiz upgrade helper present first time in 2.3.x, 2.7 major change in themes if known can address at the 2.6 stage of the march. Note: cannot say if done this way, 100% no issues as every site I've ever marched was different. :\
OR, rebuild courses in a fresh 3.highest. Advantage of this ... there has been enough change to Moodle where a little re-training for teachers would be in order anyway. Rebuilding courses would require re-learning and might result in arriving at destination in better shape (so to speak) ... might even cause teachers to re-think course design/methods, etc..
On going the option 2 route, teachers can re-acquire files contained in their 1.9.x old course by unzipping the backup and they can find their files by humanly re-cognizable names.
'spirit of sharing', Ken