The AMX Administrator command line interface (CLI) config files - 

$TIBCO_HOME/administrator/3.3/samples/admin-scripts-base.xml
$TIBCO_HOME/administrator/3.3/scripts/basic_cli.xml

may get overwritten by the TIBCO ActiveMatrix BPM upgrade if - 

1. TIBCO ActiveMatrix BPM is upgraded to a version that is using the same TIBCO ActiveMatrix Platform version, and
2. A later hotfix of TIBCO ActiveMatrix Platform is already applied on the environment which is not bundled by the AMX BPM installer. 

For e.g., In an environment with AMX v3.3.0 HF 15 and BPM v3.1.0 HF 4, the above 2 files would contain references such as - 

<import file="${admin.cli.scripts.directory}/classpath_amxadministrator_3.3.0.HF15.xml" />
<import file="${admin.cli.scripts.directory}/classpath_jms_3.3.0.HF15.xml" />
<import file="${admin.cli.scripts.directory}/classpath_soap_3.3.0.HF15.xml" />

If this environment is to be upgraded to AMX v3.3.0 HF 15 and BPM v4.1.0, upgrade steps will include - 

1. Install the new AMX BPM v4.1.0 in TIBCO_HOME
2. Run TCT to Upgrade TIBCO ActiveMatrix BPM Instance

Since BPM v4.1.0 bundles base version AMX v3.3.0 (with no hotfixes), the previously mentioned references would be overwritten to -

<import file="${admin.cli.scripts.directory}/classpath_amxadministrator_3.3.0.xml" />
<import file="${admin.cli.scripts.directory}/classpath_jms_3.3.0.xml" />
<import file="${admin.cli.scripts.directory}/classpath_soap_3.3.0.xml" />

The resolution would be - 

- Prior to installing the new AMX BPM version, take a backup of these 2 files
- After installing the new AMX BPM version, restore these 2 files. 

Hence, the upgrade steps mentioned in the above example would be changed to - 

1. Take a backup of the 2 files - 

$TIBCO_HOME/administrator/3.3/samples/admin-scripts-base.xml
$TIBCO_HOME/administrator/3.3/scripts/basic_cli.xml

2. Install the new AMX BPM v4.1.0 in TIBCO_HOME

3. Restore the 2 files from the backup taken in pt #1 above

4. Run TCT to Upgrade TIBCO ActiveMatrix BPM Instance
 

TIBCO ActiveMatrix BPM upgrade may require an additional step to restore ActiveMatrix Administrator command line interface

admin-scripts-base.xml, basic_cli.xml