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I also faced this issue, but when you build a foundation nearby and then come back again to the place you want to build you can build it again.

Yes, I faced it too. Not only when you exit the game, but also when you go to some other place on your raft and come back the water cans or the water purifiers were gone. I posted this issue already earlier in the comments. This issue started to appear when I downloaded the Version 1.04 update.

No, the developer had mentioned that the older versions of game won't be compatible. may be the developer will fix this issue in some later updates.

I built 6 water purifiers on the foundation and started cooking salt water on it and after sometime 2 out of the 6 water purifiers did not have any water cans on them. They were gone without me doing anything. I thought may be I had removed them and forgotten so I looked in my inventory and chests but they were not even there. This thing happened 2 times. Then I removed 2 them and built 4 more water purifiers on the floor above the foundation and I had 4 of the previous ones on the foundation. Then the shark attacked so i had to go and then when I came back on the above floor, poof! 3 of the 4 purifiers were gone without any trace.

Now I cannot keep more than 5 purifiers on my raft because of this and as my raft is pretty big now so I have to go all the way to where I put my purifiers whenever I get thirsty.

Please look into this bug.

I use windows 10, 64 bit PC and I downloaded the 64 bit version of the game. This issue started to appear when I downloaded the Version 1.04 update.