I can identify two cases with distinct outcomes: (1) your item familiar is destroyed or permanently lost, and (2) your item familiar is lost but later regained, after a period greater than one day per level.If your item familiar is destroyed or permanently lost:
When you replace it, you have a new item familiar, which is not the same as the old one. You have not invested any skill points or spell slots into the new item familiar; you invested them into the old one. There is no way to recover the skill points or spell slots you invested, and you have to start all over again with the new item familiar. Note:
You may replace a lost or destroyed item familiar after you have advanced one level, as if you were gaining an item familiar for the first time.
and observe that, when you gain an item familiar for the first time, it doesn't have anything invested in it.If you lose your item familiar, but then find it again:
In this case, it depends on your reading of "you automatically lose ... all benefits derived from possessing the linked item (plus any resources you put into the item)." In one interpretation, this is just reminding the reader of the consequences of losing an item which had provided a bonus -- while the item is not in your possession, it does not grant you bonuses, you cannot activate its abilities, and so on. However, if the item is restored to your possession, you regain its benefits. The argument against this interpretation is that you are only said to lose the benefits of your item familiar after it has been out of your possession for several days, which is not a typical feature of a loss of benefits of this sort. Additionally, there is no matching reminder that you regain its benefits when you regain the item.
In another interpretation, this is a special feature of item familiars: when you go several days without your item familiar, you indefinitely lose the ability to access its benefits. Of course, no provision is made for you to regain access to its benefits, so by "indefinitely" I really mean "permanently". You cannot ever recover the ability to use or benefit from your item familiar, nor can you get back the resources you invested in it, either for their usual uses or to invest them into another item familiar. However, you still have an item familiar (it just doesn't give you any benefit), so you can't get a new one. You must destroy your own item familiar, again losing 200 XP per level (and permanently this time), to give yourself the opportunity to replace it.