1) Based on the information you have provided, my suggestion would be that the allocations for vacation payable was not turned on at the account level until Sep/22.  Each account can or does not have to be allocated even though it is part of the journal entry.  If wages was allocated before Sep and Vacation payable was not, then the Allow Project Allocations option on the account was likely not turned on before Sep.

2) No, that would have to be done with custom programming.  It is not part of Sage 50.  However, you can run the Project Allocation Detail report for all projects for the date range, dump it to Excel and also dump the General Ledger report for all accounts to Excel.  Then use some lookup or index/match formulas to identify which entries were or were not allocated to projects.  You could use this as a template and then copy and paste new data in as you move through the years.

If you are using Quantum, then there is an Unallocated Amounts report.  If not, then if you are working with a consultant or bookkeeper that is part of the partner program, you could ask them to run the report for you.