Hello,
First note that the use of '-target_epsg 3949' will result in a reprojection and the '-target_precision 0.001' only has an effect in case of a reprojection. If you only want to set the EPSG code then please use just '-epsg 3949'.
In theory it is possible to set a VLR in-place without rewriting the file. This assumes that there are some free bytes after the header that are not already occupied by other VLRs. If you run lasinfo (the only tool that supports a few in-place edits) you should see something like "user bytes after header" and if those are enough bytes for your VLR then this cpuld be possible (but not implemented yet). If you want to override an existing projection VLR then it just would need to be smaller or equal size if there are no "user bytes after header" (but also not implemented yet).
Can you send a lasinfo report?
Martin
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