On our SMP server, we have some commandblock sets for various things. Every now n' then, we have to shuffle the commands to make sure they work, because their previous location essentially locks down the command, making it unable to run. 
It doesn't work to turn it to "Needs Redstone" and back.
It doesn't work to turn it to "Impulse" and back to Repeat/Chain blocks.
It doesn't work to replace the block with a new block and a new command.
It doesn't work unless I move the blocks to an unused block space -even if it's just one block space away.

 I took a video of this, but this is not viewable here, so here: https://www.reddit.com/r/MinecraftCommands/comments/izru4o/why_are_command_sets_like_this_this_was_working/

Attached is a screenshot from the server, where the problems are inside some module towers I have that surround an area, where many are actually operating perfectly fine, but enough of them are not.