This error can occur if you have 2 different scenarios replicating from the same directory on your master. 1 of the scenarios may have some include or exclude filters for that common root directory while the other scenario has no filters added. Because both of these scenarios will use the same data collector folder if 1 of them has include or exclude filters and the other does not this can cause RHA to throw this error.
One method to resolve this issue is to combine the scenarios so there is just 1 scenario replicating from that root directory on the master. A customer recently had this error and both his scenarios had no filters applied but after combining the 2 scenarios into 1 the error stopped.
If you cannot combine the scenarios if possible apply the same include or exclude filters to all the scenarios that use this same root directory on the master.
If you cannot do either of the above solutions you could schedule these scenarios so they sync at different times and are not running at the same time using different filters. For more info on setting up your scenarios in scheduled sync mode see the following article: