Has this happen to several of our ls members and myself, so I can give first hand information.

ISP: Karoo
Type of Internet Connection: DSL
Internet Connection Speed: 6mbps
Date & Time:
Frequency: Almost always.
Character Name: Coco Estheim
Race: Elezen
World: Balmung
Class/Level: 50 CNJ (WHM)
Area and Coordinates: Camp Skull Valley
Party or Solo: Solo
NPC Name: N/A
Monster Name: N/A
In-Game Time:
Steps:
<*Add more steps if necessary.>

As the problem isn't 100% reproducable, you can't really detail it in steps. What happens is, in and around the Skull Valley area, linkshells will sometimes be unequipped and you'll be unable to type in them or change to another linkshell. One instance I temp-logged (went to character select screen) and came back to find it had deleted my linkshell. I was still in the ls list according to another member. Couldn't see ls chat. Couldn't receive a new pearl as I already had one (apparently). The only way to solve it was to exile me and then give me another pearl.

Another instance, I was riding past Skull Valley and noticed that my linkshell automatically changed itself to the top linkshell in my list. Upon reaching Bald Knoll I was able to change back and everything appeared fine.

Someone in my linkshell has had this issue two days in a row now. Happens whenever he is mining in the area and he says he has to leave Skull Valley and log somewhere else. Then it will sometimes come back and work normally again.

Basically, if it happens - do NOT log out in Skull Valley as there's a high chance your linkshell will be deleted and you'll have to be exiled / reinvited.