Incremental Compilation and SignalTap

That's not good. For skyjuice, the PostFit filter in SignalTap is only a filter for finding node names and has no affect on what's done in the next compile. Quite often the same node name(such as a register) can be found in pre-synthesis, post-syntesis, post-fit SignalTap, etc. filters in SignalTap and they all act the same. If you want to preserve it's location then you need to use partitions. (Also, don't forget about trying Rapid Recompile)

Note that most of the time you don't need b), as most issues are functional issues that should occur even if everything is placed-and-routed again. The main time b) comes up is with incorrect design/timing constraints, such as something that is incorrectly false path'd, and on one fit it happens to meet timing and work while on another fit it doesn't, but you never know because you false path'd it. SignalTap is invaluable for tracking these things down, but most problems don't fall into this category. (Or at least hopefully they don't and I would revisit your timing constraint methodology...)