It was a fault at my end. The problem was:
an issue is already in "In Progress" status and I removed all the transitions associated with that status. Therefore there was no workflow appearing further for all the issues which are in "In Progress" status. I just created a new workflow and assigned my project to the new one.
if you are facing only for specific issues then you can do Integrity Checker, check this for more info
if you have same behaviour for all issues check anyconditions are added and also check close and resolve permission on project permission scheme
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