I had exactly the same thing happen to my 1990 Yanmar 3GM30 with about 2000 hrs on it. During the summer the coolant level was at the low end of the mark on the reservoir. But it was not loosing coolant, as far as I could tell and so it was not a problem. Last fall I did the usual engine maintenance; change oil, filters, check belts, impellor, etc. And I completely cleaned the engine bilge. We purchased the boat last summer and this was the first time I had to address the oilly bilge. The boat sat in the water, at our dock in NC, all winter (such as winter is down there, but we did have some freezing temp nights this year). We are not there, but I have a neighbor watching the boat. The bilge has been dry all winter but about a month ago he noticed there was coolant in the engine bilge, but he could not find a cracked hose or any leak. I was down to NC a couple of weeks ago to check on things and I noticed that the bottom of the reservoir plastic container was wet with coolant, yet it was empty!. I opened the fill on the engine and it was full?!? Of course the engine was cold. I thought maybe I had a cracked plastic reservoir, but I could not find any leak. And just like RikHall the reservoir is higher than the engine fill. I added coolant to the reservoir up to the mid point and ran the engine for awhile. All seemed fine, there was no additional leak???
I had to edit this part as I re-read what Rikhall's suggested. He is suggesting the coolant just siphoned out of the reservoir, not out of the engine. I would agree as my engine was still full, the reservoir was empty and the amount in the bilge was about as much as was in the reservoir (nearly empty) to begin with (but I did not measure it). I am rusty on my PV=NRT and I don't have an explanation on how the coolant would syphon and overflow? I had suspected that the cold opened up the seam in the plastic bottle and it just leaked out the bottom, but I could not find anything wrong with the reservoir bottle.
I left this as a mystery to be solved when I was down there and probably after I got some sailiing time in (priorities).
Any other inputs to this puzzle are welcome. I also believe your engine is fine.