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I enter a transaction in the account of my main node to transfer 100 to the account of another node. As I am not mining a pending transactions is created, which I see in my overview including a transaction id/hash. When I stop the geth the process for my main node and restart the geth process the pending transactions has dissapeared and is not in my list anymore. When I start mining nothing is processed, so the 100 is never transferred. Is this correct behavior?

ps. if I do not restart my mainnode and start mining the pending transactions are correctly processed, so the processing of pending transactions itself is not the issue

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Yes, that's normal Geth behavior.

eth.pendingTransactions are the transactions that your local Geth node has, that haven't been mined to a block. Geth does not persist these anywhere, so they are gone when Geth is restarted.

You can also see that eth.pendingTransactions is an addition to Geth and not part of web3.eth. (There's also eth.pendingTransactions vs eth.getBlock('pending').transactions.)

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