There is some previous posts regarding this: Markers in analyzer should be persistent . Essentially, the whole input file is being reparsed and all tree nodes are flushed whenever filter settings change or when a new file is re-opened. We have not found a reliable and cost-effective to maintain the markers between parsing sessions. We keep feature additions down in order to sell the 1480A unit for the low $399 price.
We are considering incorporating the more advanced features into a separate for-pay software. This would allow a low base price but with an upgrade path for advanced users.