Additional PHP directives disappeared when the subscription was synchronized with a service plan.
Subscription is not in the locked state.
It is expected behavior.
Additional PHP directives" settings from a Service Plan will become the default ones for objects of lower levels. In other words, settings configured on the service plan level will become the default for all subscriptions based on that service plan, and settings configured on the subscription level will become the default for all domains based on that subscription.
A subscription will be in a "locked" state if there were some changes in it that are clearly forbidden for a customer according to the Service Plan permission settings. Since Service Plan cannot provide permissions for customers to modify additional PHP directives any changes in "Additional PHP directives" settings will not lock subscription.
As a workaround apply either one of the following:
Use custom settings in Home > Subscriptions > example.com > Change plan/add-ons > New service plan for subscriptions that need additional PHP directives.
It will require making any change for every subscription separately.
Add required additional PHP directives to the current service plan in Home > Service Plan > select the corresponding service plan > PHP Settings > Additional directives.
Additional PHP directives will be propagated to all subscriptions linked with the service plan.
Alternatively, it can be done as well through Service Plan Addons in Service Plans > Hosting(Reseller) Plans > Add an Add-on, Configure the addon by specifying required PHP directives and apply this addon to the desired subscription.