How do you save a effect or transition from a template?
For me I select the effect normally in the panel or in the composition and save the animation preset and rename it when I apply the animation preset to another project it doesn't apply correctly it doesn't have all the properties in the effect.
Basically it's applying the default effect instead of the custom effect I selected
Is there any way I can save transitions and effects from a template without the effect going back to default?
Reveal the changed properties in the timeline using the UU shortcut, select them and then save the preset. That aside, templates often use all kind of trickery like expressions or referencing effects from other layers, so there may not always be a way to completely retrieve the magic just by saving a preset.