so now i need to upgrade again, but this time it's not a fresh system. if i go straight from 10.3 to 13.1 ...
Please ask for advice for how to do such a giant upgrade in place. I've never done it, so I won't give you advice. Just a little story: About 5 years ago, I had fallen behind by two major version (I think from 9.x to 11.x), and based on the advice here, I decided to not do an upgrade, but a full reinstall of the OS (but keeping the data disks in place, those are on separate drives). YMMV, obviously.
One of the ways to prevent upgrades from turning into reinstalls (and for your system, that advice might be too late): When editing config files that are supplied in base (for example/etc/rc.local, /etc/crontab, /etc/*/*.conf), do minimal changes, leave the copyright notice at the top alone, and do not change the formatting. Yes, I understand that we all have our personal ways we like to indent and format things, but if you have changed every line, then the merging tool (which tries to combine the changes you made with the changes coming from the update) will likely fail, and you'll have to update the configurations manually.
The important part to remember is that FreeBSD upgrades works on two things separately. One is upgrading the base OS, which does not include most major applications or servers, such as perl and apache. The second one is upgrading the packages (or ports, same concept different install/upgrade mechanism). The two are quite decoupled.
And if you do lots and lots of package updates, your cache directory for these updates will eventually use lots of disk space. Use "pkg clean" to fix that.
... will email and web server stop working? perl scripts? ssh and sftp?
As Martin already said: I would expect most things to simply work. My current system has been upgraded from 11.1 to 12.3, and most version upgrades (about half a dozen), absolutely nothing broke. Most of the time, my entries in the sys admin log file are "upgraded to 12.X and updated packages, boring". Sometimes, upgrading a package causes incompatibility with older configurations; the example of apache is good, because I had that happen. Same with Samba. Sometimes packages no longer exist, and you need to install newer versions that have different names (for example bind91 -> bind911). The other source of upgrade incompatibilities that I experience is Python: You may have hand-installed (perhaps using pip) special python libraries that are specific to version 3.X, and are not installed yet (and perhaps not even available) in version 3.Y. The same can happen with perl. In most of these cases, just re-installing things fixes the problem.
also, if it's running, can i assume the file system is ok?
If it passes fsck once, it is as OK as can be.
