If you upgrade some of your instances to V9.5 and the remaining stay at 8.2,You might see this issue.db2ilist lists the instances that are at the current instance level.Lets suppose you have db2inst1,db2inst2 and db2inst3 and only db2inst3 is upgraded to V9.5 and remaining are at 8.2.If you are attached to db2inst3 and if you hit db2ilist,you would only see db2inst3 there.
There is a workaround for this problem.You can use the db2greg utility and parse the verbose output.Below is an example that i used to list all instances that start with 'db2inst' prefix:
db2greg -dump -v grep -i db2inst cut -d',' -f4
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