Every scenery object has a bounding box defined in its model. This is the red box shown by Instant Scenery when you select the object for moving.
When FSX loads scenery, it removes autogen scenery inside bounding boxes of all placed objects. This is probably the reason why many trees are missing when you load the scenery.
Instant Scenery doesn't mimic this behavior. When you load a BGL file into Instant Scenery, it "hides" it from FSX and instructs FSX to reload all scenery files. The objects from this BGL files are then drawn by IS and not by FSX until you close FSX.
So this is why you get all of your autogen back after you load the BGL into IS.
You can tell FSX not to exclude any autogen under the object by going into the Move/Delete Objects mode, selecting an object, clicking Options, selecting This object and checking Do not remove autogen scenery under the object.
Sadly, there is no way to apply this setting to a batch of objects with a single command in IS. If you have placed lots of objects, you may want to decompile the XML file and add the <NoAutogenSuppression> XML tag for each object, then recompile the BGL again. Instant Scenery will allow editing the recompiled BGL, provided that you don't add anything else with BGLCOMP.