That is considered quite normal, use a Custom POI category to save your locations in as its more robust and can survive a map update with no issues, it also lets you put the file on to any other TomTom product should you ever upgrade etc. - Mike
They won't disappear once the 540S gets updated to the 9.x application. The 140 and 340 were already upgraded, so hopefully the 540 upgrade is sometime soon.
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