The item.update API method resets application in the parent template. How to reproduce:

• use default "Template App Zabbix Agent" and "Template OS Windows". "Template App Zabbix Agent" is linked to "Template OS Windows".
• update application for "Agent ping" item in "Template OS Windows" (e.g. use "Zabbix agent" and add "Test")
• change update interval for "Agent ping" item in "Template App Zabbix Agent"
• check application for "Agent ping" item in "Template OS Windows". "Test" application will disappear.

Debug:

item.update [items.php:511]

Parameters:
Array
(
    [delay] => 3600
    [snmpv3_securitylevel] => 
    [authtype] => 
    [applications] => Array
        (
            [0] => 206
        )

    [itemid] => 22232
)

Cannot reproduce in 2.4 or 3.2.