Are there any rules preventing transferring runes on intelligent weapons, besides Item Agency?
\$\begingroup\$ Are you asking about adding and removing runes, or just removing? \$\endgroup\$– David GayOct 1, 2020 at 15:21
\$\begingroup\$ All of that. I mean adding, removing and transfer runes. I didn't see anything preventing that, except taht the intelligent weapon might not activate the new runes. \$\endgroup\$– MJdenisOct 1, 2020 at 17:00
Yes (with a caveat)
The rules on specific magic weapons state (CRB, p 600, emphasis mine):
These weapons have abilities far different from what can be gained by simply etching runes. A specific magic weapon lists its fundamental runes, which you can upgrade, add, or transfer as normal. You can’t etch any property runes onto a specific weapon that it doesn’t already have.
Presumably, an intelligent weapon is a specific magic weapon, and thus cannot have any property runes added to it. There doesn't seem to be anything preventing their removal, though. It's worth discussing options with your GM.