I have to firstly assume  that it is not any filewall rule in your network infrastructure that disallow traffic and/or file read/write permission (for the Win-Server user/admin account used to install your MobiControl server modules) in the referenced file-sync folder(s) on the server side.  

Are the source/destination folder(s) referenced in your file-sync rule residing in a network file-system accessible (i.e. read and write permissions)  by ALL your deployment servers in your HA system?  If not, you have to make it so in the most general case in which ANY devices can be managed by ANY available DS at any time.

Alternatively, if your deployment servers and devices are physically separated clearly (e.g. group "A" devices only managed by DS "A" and  group "B" devices only managed by DS "B", etc.), and you have Server folders "A" accessible by DS "A", and Server folders "B" accessible by DS "B"), then you might try using two file-sync rules to handle the two groups.  More importantly, you have to change the "server priority"  advanced-configuration for the device/device-group such that DS "A" has the highest priority to manage group "A" devices and DS "B" has the highest priority to manage group "B" devices.

You can solve this by having the same folder structure and files on both DS1 and DS2.

The file(s) has to be on "C:\%foldername%\" on both DS1 and DS2. 

In the file sync rule, set "C:\%foldername%\". The device will look here which ever DS it is connected to.

If there are no firewall rules or similar that prevents this, it will work. I have the same setup.