Steps to reproduce:
1. Create 2 hosts and link Template with Trigger to those hosts
2. Add trigger dependency: Host2 Template:Trigger depends from Host1 Template:Trigger
3. Import Template with checked checkbox "Update existing triggers"
4. Trigger dependency on Host2 deleted.

My actions:
1. I created Host1, Host2 with linked template "Unified RCU".
2. At Host2 i created dependency of trigger "Unified RCU: ??? ?????? ? ??????? {$WAITTIME} ??????." on Host1 trigger "Unified RCU: ??? ?????? ? ??????? {$WAITTIME} ??????."
3. Then i imported template XML into Zabbix with default import settings.
4. Trigger dependency of Host2 disappeared.

I have this bug on Zabbix 2.0.9, 3.0.6 and 3.0.13.
Template attached to bugreport.
Trigger with problem is "Unified RCU: ??? ?????? ? ??????? {$WAITTIME} ??????.".