Correct me if I’ve gotten this all wrong. I think what you’re describing is either: a Master hiding their Padawan’s Force presence (or vice versa) and then being unable to communicate through their bond; or a Master or Padawan having their Force presence hidden by someone else and then having the same thing happen. Let’s see if we can come to an answer for both.
First off, both are plausible scenarios. Jedi can have their Force presence hidden by another Jedi or they can do it themselves. I know that this happens several times in the EU, but I’m blanking on specific examples. While I don’t think I’ve ever heard of this interfering with a Jedi’s ability to use the Force, you have discretion over the character’s strengths and weaknesses; perhaps they weren’t too good at communicating through the Force in the first place, and having their Force presence blocked only made it harder. Your choice, really.
Master-Padawan bonds are often quite strong, and I would guess that if one really wanted to call out to the other then having their Force presence hidden wouldn’t stop them. However, if one Jedi was trying to contact a Jedi who had hidden their presence (depending on various things like the strength of their bond, physical distance, how well they’ve been hidden) they may find it impossible, because it is doubtful they’d be able to locate or lock onto their presence to actually send a message.
The Jedi being hidden would probably experience little to no change in their ability to use the Force. I can’t recall an instance of this happening. But, there are always extenuating circumstances, and you could probably make it work if you needed to.
Now: if it was, for example, a Master hiding their Padawan’s presence, I should think that they wouldn’t have as much trouble communicating or finding each other. The Master should be able to feel the Padawan in order to keep hiding them, as I’m pretty sure masking one’s presence isn’t a quick one-time thing (correct me if I’m wrong). If it were someone else hiding either the Master’s or the Padawan’s presence, they could plausibly have more trouble contacting each other, as I’ve already said.
I’ve gone in circles a little bit but basically: it is possible to hide a Jedi’s Force presence, the Jedi being hidden should not have trouble using the Force, and any other Jedi (except the one hiding their presence, if they aren’t doing it themselves) may not be able to contact them through the Force.
I hope that helps! There aren’t a lot of specific rules when it comes to the Force, so you have a lot of creative liberty here.
~ Jacen