Here are some of the potential issues with encrypting Linux after the initial installation:
Resizing the filesystem - shrinking a filesystem without corrupting data.
Handling disk layout - maintaining consistent mapping between physical and virtual chunks.
Data integrity - to verify that the data written back matches the original.
For example, the first step when enabling in-place encryption is to resize the partition, move the existing data, and free up as much space as possible. After that, we enable encryption on the freed space. Once encryption is successfully enabled, we can then move the data to the encrypted partition. The challenge in this first step is dealing with insufficient disk space when we can't move the data because there isn't enough free space. One potential approach could be to resize and encrypt the data block by block, moving data to the encrypted block as we go. This first step is quite complex.