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Hi,
If it is only a few trees missing, it's sometimes better just to plant a few library object trees in the bare spots.
Compiling in groups doesn't prevent autogen suppression. Groups only minimize suppression.Compile with the latest release (0.0.96(q)) doesn't prevent autogen from disappearing, even with 100m groups.

whatever you are using to generate autogen in the vicinity of the runway/aprons.

Jacques, a screenshot of your ADE display doesn't help me much. What I asked for, and what I need is
There appears to be a large default flatten that is inhibiting all autogen over a wide area. Unless I have the file that you are using to replace that autogen, there's little more I can do but assure you that, if you compiled in 100m groups, autogen suppression due directly to the GP bounding boxes will not extend beyond about 70 me from the edge of any GP item.
While I'm not disbelieving you that autogen is being suppressed further away than that, I suspect that what you are experiencing is some indirect effect. For example, if you've used some utility to replace the autogen, perhaps a simple overlap of some portion of the bounding box and the area to be covered with autogen is sufficient to suppress autogen generation over the entire area.
Without the files to generate the same autogen that is being suppressed, there's nothing more I can do.
Don