I faced this issue when working on my HP Pavilion x2 which has a touchscreen. The mouse pointer disappeared when moved over the Chrome but continued to show up in other applications. It seems to be related to the hardware acceleration settings and seems to have been around for quite a while on various Windows devices ranging from the HP Envy to the Surface and affecting both Windows 8.x and 10 (2 years at least going by the Google Group thread).
Anyway, the fix seems to be to disable Hardware Acceleration in the Advanced Settings of Chrome:
Go to Chrome Settings > System and uncheck the following –Use hardware acceleration when available
Also, hardware acceleration does seem to be buggy on Chrome causing a range of problems related to mouse pointer lags, at least on Intel GPUs going by this post (came up as the top result when searching for “Chrome hardware acceleration“).