I think the problem with saved charts is that they rely on record ID numbers to identify the individuals who are to appear in the chart.  When you merge two projects the 'main' project retains its Record IDs but the 'other' project (the one you are merging into the main project) has to have new ID numbers assigned to its records because there cannot be duplicate ID numbers.  As far as I remember (apologies if this is not correct, and I haven't tried it in V7)  saved charts in the 'main' project will still work because its record numbers are unchanged.

As for other parts of the projects, the important thing to remember is to check ALL the tabs in the merge dialogue, to ensure that ALL types of record are merged where appropriate. A common mistake is to look only at the Individuals tab and then discover afterwards that there are duplicate family records, sources, etc.

Lorna