It’s one of the common problems I have seen recently : All of a sudden some of the BizTalk performance counters disappear from the list. Here are the checklist of things you can do
1. Make sure the host instances are running. If they are not running some of the host related counters wont show up in the list
In some place the performance counter could be corrupted, there are 2 useful documents I found that fixes this issue
If you still experience the problem, try running the following command
That basically rebuild the perf registry strings and info from scratch based on the current registry settings and backup INI files.