(H)and (C)ounted (P)aper (B)allots
For hand counts of secret ballot elections, EIP fully endorses and supports Peg Cage’s Glass Box Voting process and that’s what we recommend for the hand counting of paper ballots. For other types of elections (anonymous or Roll Call), hand counts are unnecessary and probably not the best option (primarily because they cannot be accomplished in a fully remote manner, but also for cost, training and other reasons). But they can still be used by those who prefer them, of course.
As an optional augmentation to any hand count process, we recommend attaching a VTN (Vote Tracking Number) to each ballot.
That process is documented here:

Activity Diagram for an EIP-enhanced Hand Count (EIP-HCPB)
Ideally, the token (VTN) would be pre-printed on the paper ballot and with it an additional detachable portion the voter could take with them. Alternatively, they could always just take a picture of their ballot from their phone.
Now you can find your ballot and that’s great. But in the hand count scenario, the VTN does nothing to ensure that your particular ballot was counted correctly. Well, that’s why hand counts have a teller committee. So attaching a VTN is not a requirement. It's really just an enhancement, it’s helpful not only for locating ballots, but it also helps to prevent fraud and to offer vote remedy.
If you want to absolutely guarantee that your vote was counted - and that it was counted accurately - then you have to use the electronic ballot version of EIP. But if you trust the teller committee and that’s good enough for you, or, if you just would rather use paper than machines, then just use EIP-HCPB without the VTN augmentation.
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* NOTE: There may be statutes in various jurisdictions that do not allow modifying the ballot in any way (like it's some kind of sacred document), and in these cases, skip this augmentation altogether and just go with the HCPB process as normal. Better yet, alter and remove these types of ridiculous statutes. They serve no valid purpose and in fact aid in the disenfranchisement of voters everywhere.