What I'm saying is that in a situation where someone has been missing for a few weeks and hasn't actually said anything at all (and thus, has not said she/he isn't coming back), her/his character(s) should be moved off the plotship and left somewhere out of harm's way (but not somewhere from which they cannot easily join a new plotship (or return to their old one if it's still around) if and when the player comes back).
Example: Suppose Xerena has one character, Kusanagi, serving on YSS Tachikoma under Taii Aramaki.
Situation: Xerena has been absent for about 3 weeks. She did not tell anyone in advance that she would be away, either temporarily or permanently. After the first 2 weeks or so, the YSS Tachikoma plot GM sends her an e-mail, to which she has not yet replied.
Recommended Action: Have Kusanagi transferred off the YSS Tatchkoma to an offstage background position, where she will stay until Xerena returns. Send a private message to her account so that if and when Xerena returns, she will be aware of her character's status. For the time being, assume that, since her transfer, Kusanagi has been leading a rather uneventful career, keeping a safe distance from the action of any active plots. In her spare time, she practices those skills she is not using in her day-to-day life (like anything combat-related) so as not to lose her edge, but not with enough intensity to noticeably improve them.
When Xerena comes back, she has Kusanagi request a transfer back to the YSS Tachikoma, or perhaps to another plot. If necessary (and it may well be if returning to the Tachikoma), Xerena and the appropriate plot GM(s), and any other players whose characters may be affected, can discuss the details of Kusanagi's return (for example, whether Kusanagi will be resuming her old station - both Aramaki, the captain of the YSS Tachikoma, and Togusa, who took over Kusanagi's duties when she left, might have things to say about that; in fact, that issue might be best dealt with ICly).
Of course, it is entirely possible that the YSS Tachikoma got blown to bits - with Kusanagi onboard - within those first 2-3 weeks, but Kusanagi shouldn't be left aboard the YSS Tachikoma for months on end - she should await Xerena's return in a place that isn't a target.
Note: The ship and character names, which were all taken from a certain anime, are used purely as examples, and are not (to my knowledge) used by any actual SARP characters or ships.