I would suggest using a program like Delta Patcher which you can get from there release on github.
and following a guide like the one posted here at Ninten's Blog
I am releasing these as Delta patches because this way I am not going to break anyone's TOS/Copyright.
Navmesh Fixes were done following the mnikjom's guide:
Fixing Deleted NavMeshes
Arissa - The Wandering Rouge was ported to SSE following the video at
Skyrim SE Port Arissa Follower ESM / ESP + NIF Conversion
and additional fixes from Arissa for SSE. . . The last thorn in my side.
Hermit Mountain Cottage - A buildable Home
Version: V6.0a
-Fixed Navmesh

Red Rose Mill
Version: 1.2.1
The Optional File
-Fixed Navmesh

Aurlyn Dawnstone - The Reclusive Philosopher
Version: Aurlyn Dawnstone - Update - SSE 7.30.03
-Fixed Navmesh

Khajiit Will Follow
Version: 4.6.1
-Fixed Navmesh

Miraak - Dragonborn Follower Dialogue Overhaul
Version: 1.71
-Fixed Navmesh

Breezehome
Version: 1.6
-Fixed Navmesh

Original File Checksums
(Use these to check that you apply the patch to the right file)
File: CompanionArissa.bsa
CRC-32: 01cc0183
MD4: 2234131aa1ae6bdbb1e8c071ff507ef8
MD5: ba04382a1f115f470b7f2fd1c78e8534
SHA-1: ea2099af057c14b590be70ed6962f3120caca7bf
File: CompanionArissa.esm
CRC-32: c4ae95c0
MD4: c03580d004cb2cc617d45499764bfbee
MD5: d2217dd365fff9bec7ce58ee7d68a3d9
SHA-1: 54397e50d9bc1bf674443f6dd75b57d17340bff7
File: Hermit Mountain Cottage.esp
CRC-32: 928f3fa7
MD4: bb99cb53797c2c6be259d47765b22957
MD5: b0bd848fad72b48240615640c5d1cf56
SHA-1: c1ec2008b14d77bdd78124c3819e99536b2d90ec
File: RedRoseMill.esp
CRC-32: c3618e92
MD4: ba5f3d303bd6c9370e99030db0985f17
MD5: f539adfdec723154f455437e5f2db011
SHA-1: 1674bbc7810508c72b04bafec62423295fb99afe
File: Aurlyn.esp
CRC-32: 326ff596
MD4: c6dbe1b1cf04ec1c853f58a65e27abcd
MD5: 181e6129d9b284c7512f5ee8b173158d
SHA-1: b4224bf7f120933cb8499026e40a2e4f29de200f
File: KhajiitWillFollow.esp
CRC-32: e7575d1b
MD4: 45966693a2ffd5ef3abaec8dd7f5a3b7
MD5: 2b4fb0283f2b1d35452ed28fba2f18fe
SHA-1: b02004b77110f60b2837919edd6e2a322d04389d
File: MiraakFollower.esp
CRC-32: 5b38f3f0
MD4: f071ac353df5387a3eb9e2dd7c3a211d
MD5: d56d3cb59b0d4cbd9d7178cd19e313b6
SHA-1: c72b50e718a427e18db50c96354b6e4e3b91d471
File: Eli_Breezehome.esp
CRC-32: 4768b826
MD4: 35ed30534588269f975e0ab2758d17cb
MD5: 7a0f046c668e3d3cee6f81f7ee92f0e9
SHA-1: 4c62129a5c9620a7fc4f91343f4f0b65f50968f2