I've been using DLP-Link glasses for a while now, source is via a HTPC.
The display can sync the glasses, but it doesn't know which frame is supposed to be first, hence the reason displays (and software players) have the "reverse" mode.
For instance, I can play a stereoscopic clip with Stereoscopic Player under default settings, and I have to set my display to "Mode 2" (which is reverse). Playing the same clip with PDVD10 or TMT3, I set my display to "Mode 1".
With that said, it's always the same. Everything I play with PDVD/TMT3 is always "Mode 1" and vice versa with SP. Also, it doesn't make a difference if I pause a movie or skip ahead or back, I never have to change the original Mode.
This goes for IR glasses also.
And I don't think anyone would be able to watch more than 30 seconds of any 3D video with it being reversed, the viewer can tell right away if it's not correct.
In a nutshell, this isn't a big deal, and it isn't anything new to DLP-Link or IR-based glasses, been this way since the beginning.
The only problem I can see is with PC games that have built-in Stereoscopic support (like the Avatar game). It could vary from game to game.
I'd also like to add, before I got a graphics card that supported MVC hardware decoding, I had to decode via the CPU. Sometimes, a particular scene would be too much for the CPU, and I'd get stuttering. Never once did the glasses lose sync or get things reversed due to this.
Vizio P65-C1 (2016)
JBL Studio Series (Front, Center, Right), JBL 250W Sub, Kenwood Rears, Onkyo Atmos Upfiring
LG UP970 UHD Player
Nvidia Shield TV