Uhh ... one should never 'copy over the top' or 'replace files' when it comes to Moodle code directory.
When it comes to migrating a moodle ... moving to another server ... best to archive the site .. full site backup ... and get the backed up code directory, the backed up moodledata directory, and an sql dump of database onto the new server. Get it up and running first. Then tackel the upgrade(s) ... note that's upgrade(s) ... plural ... cannot 'hyperjump' a Moodle 2.0 to a 3.3 in one step. One can take Moodle through a 'march' upwards ... 2.0 -> 2.7 -> 2.9 -> 3.0 -> 3.3
Why the 'march'? There were some major changes to code which need to be checked out an one makes sure they are functioning before taking the next step. Plus ... there were upgrades to MySQL and to PHP that need to be in place before one pulls the trigger on upgrading.
Please refer to: https://docs.moodle.org/33/en/Moodle_migration
https://docs.moodle.org/dev/Releases for the PHP/MySQL requirements for versions of Moodle.
The above links kinda explain why I think Bitnami should be avoided. First, Bitnami on Linux makes no sense because Apache, MySQL and PHP can be acquired natively from the operating system repositories and whose repositoroies continue to support upgrades to the pieces that make Moodle go.
Bitnami ... is an easy install, yes, but what of upgrading say PHP or MySQL in a Bitnami package. Uhhhhh, as I understand Bitnami, one has to upgrade all of Bitnami to get an upgrade to part ... PHP/MySQL/Apache - remember your moodle code directory, and data directory are in that stuff. Make a mistale with Bitnami upgrade and you could loose it all.
Besides that, Ubuntu 16.0.4 is long term support and one can easily get updates/upgrades to any of the packages that Moodle requires to run.
One can find more support for Ubuntu 16.0.4 in tons of blogs .... Bitnami?
So, all this to say, I hope you have the backup of the 2.0 still. Migrate it to the new server first. Get it running first. Then planout/strategize the 'marching' of Moodle to your desired stopping version.
'spirit of sharing', Ken