since they are stored in a file (%hb folder%\settings\%servername%\%charname%\charactersettings.xml -> search for <EnabledPlugins>
<Entry>Anti Drown</Entry>
<Entry>Refreshment Detection</Entry>
</EnabledPlugins>, you could switch / rename files with a script and then start honorbuddy.
<HBProfile>
<!-- Sole purpose is to enable a plugin when started with Questing bot -->
<Name>Enable Plugin</Name>
<MinLevel>1</MinLevel>
<MaxLevel>200</MaxLevel>
<MinDurability>-1</MinDurability>
<MinFreeBagSlots>-1</MinFreeBagSlots>
<QuestOrder>
<CustomBehavior File="EnablePlugin" Names="NameOfPlugin" />
</QuestOrder>
</HBProfile>
Then on your HB shortcut add the arguments like so: <PathToHonorbuddyExe>\Honorbuddy.exe /noupdate /autostart /loadprofile="<PathToEnablePluginProfile>\EnablePlugin.xml" /botname="Questing"
if you have multiple CustomClasses then you may want to add the /customclass="" argument as well (set it to Singular if having issues)
This will run the profile that enables your plugin and then stop, you can do what you want from there.