This is a remarkably easy problem to solve.

From man:

The inotify API provides a mechanism for monitoring filesystem
       events.  Inotify can be used to monitor individual files, or to
       monitor directories.  When a directory is monitored, inotify will
       return events for the directory itself, and for files inside the
       directory.

The problem is a kernel based value, that determines how much memory is used by processes such as lsyncd. Lets just double check what value it is set to presently:

Check Inotify max_user_watches value presently

[root@server php]# cat /proc/sys/fs/inotify/max_user_watches
100000

Check the amount of available memory on the server to ensure it can deal with the increase

[root@server-new php]# free -m
             total       used       free     shared    buffers     cached
Mem:          7358       6577        781          1        376       2427
-/+ buffers/cache:       3773       3584
Swap:            0          0          0

The cache can be added to free, as a maximum saturation. Linux uses lots of memory it doesn’t really need for efficiency.

Each used inotify watch uses 1 kB RAM in 64 bit systems, for 32bit its half.

Increase Inotify watches to a higher value

sysctl fs.inotify.max_user_watches=200000