Hi Rizwan,
we used to have similar issues with IDOC adapter. when the system was newly built. After multiple patch updates this got normalized. It was not recurring.
In my case, the configuration used to get removed without anyone changing it or not getting saved sometimes.
check these setting and make sure, they are all set
1. NWA>Confugurations>Infrastructure>Application resources>inboundRA(Resource Adapter)
a. check what default destination is configured. XI_IDOC_DEFAULT_DESTINATION_XXX . Is working correctly in Destinations.
b. check, if multiRepository setting is correct and not changed
2. NWA>Confugurations>Infrastructure>Application resources>JavaIdocAdapter (Resource Adapter) - check CustomDestMap Class java.lang.String in Properties tab
regards,
Nazeer