If you have already performed the steps mentioned under "Deleting the Java Stack (Java Add-In) of a Dual-Stack (ABAP+Java) System Manually" then the problem shouldn't be there.
Provide the output for this command for all the nodes
ls -la /usr/sap/SID/D*
ls -la /usr/sap/SID/D36
Also provide the contents of the profiles. (if possible)
Regards
RB