In Ethereum, there are often short forks near the head of the chain because two miners found the PoW solution for new blocks at around the same time. Only one of those chains will ultimately wind up being considered the canonical chain and any blocks from non-canonical chains wind up having no effect on the state. Non-canonical blocks may wind up being added as ommers in future blocks, but everything in this article applies regardless of whether that happens.
If your transaction winds up in a non-canonical block, is it doomed for all time? Fortunately no. Most likely your transaction will still wind up being added to a block on the canonical chain even though it’s already wound up in a block on a discarded fork.
Firstly, your transaction might have been selected for both the non-canonical block and the block that wound up on the canonical chain. Those two blocks are part of different forks so the transaction may be valid on both. In that case, whichever chain gets picked your transaction is included. However, depending on which other transactions were picked and the effect they had on world state, your transaction may have done completely different things on each fork.
Secondly, it’s possible that a node saw the non-canonical block first and treated it as part of the canonical chain (because it was the best block known to it at the time). In that case, the node will have removed your transaction from the pending transaction pool because it was already processed. When the block that actually wound up on the canonical chain turns up, the node will perform a chain re-org to switch to this new block and relegate the original block to a fork. If your transaction isn’t in the canonical block, good clients will re-add it to the pending transaction pool so it can be added to a future block.
If your transaction went into a block that was always seen as non-canonical, then it wouldn’t have been removed from the transaction pool in the first place and continues to wait for a chance to get into a canonical block.
Bottom line, getting included in a non-canonical block does your transaction no harm. It will generally hang around until it makes it onto the canonical chain.