Do you use DNS servers from your ISP or public ones?
A public one, such as OpenDNS (P: 208.67.222.222, S: 208.67.220.220) has (free and commercial) filter options that will help protect your users from themselves when they click on links to bad sites.
But if you are a diehard, run your own/company DNS server and have much more control over what sites your users are able to visit at any given moment.
Or if you channel internet access from all your users through a hardware or software router device, try to find out if it supports the use of "blacklists". If that is the case, add whatever site to that blacklist and your users are protected as well. Do keep that "blacklist" up-to-date though. All of these pointers do not require you to batch edit PDF files for bad/hidden links. You might want to take inventory of new bad links in new pdf files that come in by batch/manual processing these.
Some routers even let you make a custom "landing" HTML page that is served to a user who tries to visit any link in that blacklist.
For example: I use an old AMD dual core based white-box PC with 2GByte of RAM and 3 network cards in combination with OPNsense router software (FreeBSD). I have 2 different ISPs, each using one network card, the last network card is used to connect to a big switch that provides internet to all computers hooked up to that switch (by cable or access points). A rather basic setup...but I like things simple.
You manage this OPNsense router software in your browser and gives you a lot of control about what your users can or cannot do on the either the network or the internet at any given time. Routing, NAT, Firewall, DNS, DHCP, Blacklists, VPN, graphical overviews of (current and historical) traffic, it does everything. The amount of options it comes with, might be overwhelming at first, but once it is setup as you like it...you don't want to use any other system anymore. And there are free/open source/commercial expansions available if the standard functionality isn't enough for your intents and purposes.
The OPNsense router software is a fork of the pfSense router software, which is in turn a fork of the mO0nwall software. If you are interested in playing with these software routers, there is a lot of forums and instructional videos available for free support. Especially for pfSense. But if so inclined, you also are able to buy books and premium support for whatever exotic wish (regarding network setup) you might have.
My choice of OPNsense 16.1 over pfSense 2.3 is mainly its interface. Although pfSense version 2.3 has a drastically improved interface, I just like the OPNsense one better.