have you resolved this yet?
maybe worth checking few of the passwords not stored, which is required for SAP.
a. modify the path variable where new installed path is included.
D:\IBM\ICCSAP<X>\Server\bin;D:\IBM\ICCSAP<X>\Server\bin\gskit
remove the old instance path
b. archpro -f serverpasswd, archint.cfg gets updated
c. archpro -f r3passwd, archint.cfg gets updated
d. archpro -f MASTER_KEY_FILE, new key is registered
e. you may be getting RC=CS_RC_OD_ERROR (-262) , ondemand library could not be loaded.
Modify the path variable to have the new CMOD bin directory after the old CMOD bin path variable.
start ArchPro again with option '-f dll_keystore_passwd'
f. if you get the following error(port could be different)
CSS0463I: Starting a new client to replace client 8700.
CSS0466E: Error: ArchPro detected that client 5832 terminated.
from instance/bin > client_key_gen.bat -c -p <your password>
Server keystore created.
You may still find clues from here(even though older technote)
http://www-01.ibm.com/support/docview.wss?uid=swg21969124