Fluid Filters in Ender Fluid Conduits can not be configured, unless the block the Ender Fluid Conduit is in, contains other Conduit connections.
For example, if only Ender Fluid Conduits connect to a Fluid Tank, the option will not be displayed:

If an Item Conduit is placed in the same block as the Ender Fluid Conduit, the option will be displayed:

Fluid Filter cannot be configured when it's the only connection on that side, in the block.
To always be able to configure the Fluid Filter
[pastebin/gist/etc link here]
Please update ender io and confirm if this is still the case
Confirmed in EnderIO-1.12.2-5.0.31
I have noticed that holding the filter in your hands, and crouch right clicking on it, open the filter's config
Found the bug, should be fixed soon
Most helpful comment
Found the bug, should be fixed soon