Flannery injured an elbow during Lions training at Pennyhill Park in Surrey and was unable to travel to the Republic having been widely tipped as a likely Test starter against the Springboks.
The 32-year-old then spent a large chunk of last season on the sidelines after repeatedly tearing his calf muscle as a result of nerve damage in his back.
Flannery missed Ireland's summer tour and only made his first Munster appearance of the season in Saturday's Heineken Cup thrashing of Toulon.
But what should have a been an enjoyable experience for Flannery in an outstanding team performance ended up being another demoralising afternoon.
Having come on as a replacement at Thomond Park, Flannery lasted just 15 minutes before being forced back to the dug out.
And while he is still waiting for further analysis to discover the nature of the setback, Flannery and Munster are braced for more bad news.
"It's certainly unfortunate if it is (a recurrence of the injury) because he has worked so hard to get back," said Munster head coachTony McGahan.
"He missed a significant part of last season and this was his first foray back into selection. So to be injured in the first 15 minutes of his comeback is devastating for him."