I have just re-downloaded the game and installed blood and wine (having uninstalling it when i finished hearts of stone)

My most recent save WAS after hearts of stone ended.
but now
The most recent save i have is the one from the start of hearts of stone, with the evils first soft toutches quest showing as new

is this a known glitch

No. Nothing I have heard of. The possibility exists that you have moved or deleted some saved games - or even that the time on your PC is wrong. Try looking at the save files in Windows Explorer and sort them by date.

The strange thing is
all the HOS locations have changed to ?s
but all the waypoints are discovered and i have the runewrite enhancements still on my weapons

Have you started a NG+?

dont think so

lv 44
my quest log is very very long (looks like the whole vanilla game)

only envoys wine-boys and evils first soft touches are available (HOS and BOW starter quests)

So, when you go to load your save, hover your curser over the savefile. Does the picture have the version on the bottom right and a large + sign on the bottom left?

Version - yes
plus sign - no

Then that save isn't NG+. You have searched your folder in Windows Explorer to see if there is a save file with a more recent time stamp? If that is the latest save file, then I'm out of ideas.

i have looked in
C:\Users\admin\Documents\The Witcher 3\gamesaves
is there anywhere else they would be

I have a backup but that is older than what my savegame folder has

its odd that i completed HOS and yet it is everything EXCEPT THE HOS UNIQUE ?S from the first HOS quest onwards that is deleted
(When HOS came out i started by unlocking all the ?s and waypoints and first level runewrites before starting the quests
i still have the lv 1 runewrites and waypoints
but not the ?s unique to HOS are reset to ?)

That's a weird one. There's gotta be a reason for it - I just can't think of what it could be. It is like you have started a NG+, but you haven't. Dunno

[edit] - I assume you have done all the "regular" efforts, like ensuring you have the game, DLC's and expansions updated to their latest versions...

how do i do this
and make sure its down in gog galaxy?

ps
in game it shows HOS and BAW as being installed

Good luck.