I don't have much to add, but the same thing seems to be happening in my app, for at least one of my customers. They're using Google Calendar as well, and on a Mac.
I'm currently doing some testing to see if I can recreate the bug. I'm expecting it to take a while—when I asked my customer to try to recreate it to gather some logs, it took two weeks.
I'd say it's worth filing a bug even if you don't have all the details, especially if you have sample code you can share. It may be helpful if you run a sysdiagnose as soon as possible after you notice the problem.
When the problem does happen for you, about how long does it usually take for the missing calendars to reappear? Minutes? Hours? Days? My tentative plan to work around the problem is to just keep trying periodically until the missing calendar reppears. If it takes more than a day or so, then give up.
Just wanted to add some follow up information: I haven't been able to reproduce the problem myself, but for my customer it seems the missing calendar returns less than an hour later. In one case it was missing at 11:06, still missing at 11:19, then returned at 11:44. The calendar still had the same identifier when it reappeared, so in my app that made it easy to work around the problem.