It’s not necessarily anything to worry about. You didn’t lose any structures. The only reason you might be a little concerned is if you had some sort of notation elsewhere about which tags you were interested in. (But you would have had multiple structures with the same tag, so it’d be confusing as to which one you meant.)
This sort of thing happens typically when you’re combining (or have combined) multiple silent files, each of which may have a number of structures with a given tag already. It could also occur if you had multiple processes writing to a single file (generally not a good idea, due to chances of file corruption. Write to separate files and combine after the fact) – they wouldn’t necessarily know what the other processes were doing, so may repeat tags.
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