Reinstalling the agent should only be considered as a "last resort".
Essentially, you have two options:
1. Work with another technology to push a registry update to change the value of the Disabled string in HKLM\WOW6432Node\ManageSoft Corp\ManageSoft\Usage Agent\CurrentVersion to False
2. Work with the discovery and inventory rules in the FNMS product itself. Create a new target that targets (for want of a better expression) the devices where you want to enable usage (this might be a specific subnet or a specific device/IP). When you do this, set Application usage options to Allow application usage tracking on these targets. Please also handle the other settings with care and caution. Make sure you don't inadvertently cause any problems with your agents.
A quick note on option 2. These application usage tracking options will be added to the appropriate tables in the FNMSCompliance database that determine what and how FlexNet Inventory Agents function. The FlexNet Inventory Agents across your estate will pick up these new settings when they next connect to their FlexNet Beacon to download updated policy and other configuration files. Whilst these discovery and inventory are used, primarily, for remote execution, the target configuration will also apply to locally installed FlexNet Inventory Agents provided those devices fall into that assigned target.
The key here is test this out first. If you have a test environment, do this first in that environment before proceeding into production. If you don't have a test environment, test this first on only a specific device. Don't do this on a massive subnet in a production environment without testing first.
No, you shouldn't need anything extra. The installed agent should (on Windows) already be running in local system context. Credentials in the Password Manager are only used for remote acitvities, not for agents fully installed.