I have investigated this and found that it has not disappeared, it just that it is not being displayed properly by the Adobe SVG viewer. It does display when viewed with the Firefox browser.
However there are two complications. Firstly I found a bug in that the SVG zoom buttons are missing when no PDF version of the GenoMaps are present. This has been fixed in a revised skin available here. I am guessing that you do not have Inkscape installed on your PC and so PDF genomaps were not generated.
The second complication is that you have a large shallow and wide tree that the Adobe viewer has problems rendering and is too large for Firefox to zoom and pan efficiently. I also found that Inkscape was unable to convert SVG images of this tree to PDF again because of its size. So as recommended elsewhere in this forum I strongly suggest that you split your tree into five or more genomaps within your .gno file. Generally around 250 individuals per genomap seems to be OK. With the layout you have adopted this will be very straight forward, simply divide into vertical sections and move each section to a new genomap and then make a few minor adjustments.
If you download and install the Inkscape open source program then you will be able to generate a report with PDF and/or SVG images of your subtrees. I did a quick test with your tree split into five sections and all was OK with both SVG and PDF images. PDF images are somewhat easier to pan and zoom and most people will have a version of Adobe Acrobat viewer on their PC.