Either a 2 or a 7, no matter which way one chooses to interpret it, it makes sense. This is because this form appears to be something similar to what I would call a letter of transmittal. The purpose of such a document is to record the transfer of the items from one entity to another.
This is not a "letter of transmittal", if such a thing exists.
It is the document used when "specimens" from a crime scene are first admitted/submitted into evidence.
In this case it appears to be the transfer of the items listed on the form from the DPD to the FBI. These items were in fact transferred to the FBI on both dates (11/22/63 and 11/27/63). They were returned to the DPD (on 11/24/63, iirc) after the initial FBI examination.
If this were indeed a letter of transmittal it would include all the evidence being transferred to the FBI at that time but it does not.
As you say, the evidence had already been handed over to the FBI on the 22nd (with no letter of transmittal), and had been thoroughly tested in the laboratories in Washington. So everyone knew what evidence this was which means, if this is just a letter of transmittal, there was no need to helpfully point out that this evidence was "from 6th floor Texas School Book Depository" on the document. Everyone knew where it came from. There was no need to note the hulls came "from 6th floor window. This has already been established and has nothing to do with the transferral.
Indeed, there is no need to point out the location of this crime was "Elm + Houston", there is no need to point out the nature of the crime is "Murder" and that it occurred on "11-22-63". The FBI probably knew this already.
All these details are required if these are items being submitted as evidence from a crime scene but totally unnecessary if it is simply the transfer of evidence the FBI has already tested and already has documentation for.
Where are the "Q" numbers already assigned to the shells?
Where is the "K" number already assigned to the rifle?
They're not on this document because they are yet to be assigned to these pieces of evidence.
Why, after the signatures of Day and Studebaker, must it be noted that this evidence was "from scene"?
Is it in case the FBI had forgotten where it came from or is it because this evidence had literally just come from the scene of the crime?
We can be certain that this is not a "letter of transmittal".
It is the submission into evidence of items related to the crime in question.
Either way, the assumptions and jumping to conclusions such as two sets of shells, and that the FBI had possession of these items at 2:15pm on 11/22/63 are ridiculous.
It is definitely a source of frustration that Day writes the number "2" in different ways - one with a loop at the bottom and one without. The following is a close up of the digit in question:
Is it a two or a seven? Note at the bottom of the digit a "tail". Here is the number "7" from the document:
Note, there is no "tail" at the bottom. Here is a different number "2" from the date assigned to the "Nature of Offence":
Note the "tail" at the bottom. Certainly more pronounced but it is clear to see, the digit under question is a "2" and not a "7". In the CSS document below (again dealing with the submission of items into evidence) we see Day's penchant for using different types of "2" and we also see more examples of the number "7", without the "tail":
This document is an example of the logging of evidence, as is the document in the OP.
I would be interested to see another example of a letter of transmittal.