I dont know if this is a bug or not but after moving to the 2nd Island im missing a large Chunk of loot even the Crown jewels which is needed for the gold synthesizer Even after i built the base they still never showed up or never showed up on the World Map

Before leaving your first base, did you make sure that all of your loot was transported off the island? Anything not loaded onto the boat/chopper is gone when you leave.

This is a known issue with the release version of the game, unfortunately. (And the GOG version doesn't appear to incorporate the fix.) There are several unofficial patches floating around on the internet, several of which fix these. (My apologies, but I can't point you to a reliable site, since my favorite EG modding site is long since defunct.)

If you don't want to apply an unofficial patch, there's also a fairly simple work-around: On the first island, avoid getting any base loot items except the totem pole and the uber-loot items. The uber-loot and the totem pole should always transfer. Unfortunately, this also means most of the research tree will remain locked for you until the second island, since a lot of the best techs require base loot.