We have performed same steps at one of our clien't environment as they were removing iStore Node from their existing e-business suite.
Following steps were successfully performed without any issues.
sh adstpall.sh apps/<apps_password>
perl $AD_TOP/bin/adgentns.pl appspass=<APPSpwd> \contextfile=<CONTEXT> -removeserver
Clean up fnd_nodes table
sql> exec fnd_conc_clone.setup_clean;
Run autoconfig on remaining nodes
Change required profile options pointing to that perticular node
I hope this answers your question.