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`Could not find source file` when running in watch mode with `rollup-plugin-vue`

See original GitHub issue

What happens and why it is wrong

When running rollup in watch mode, the project will initially compile but changes to some files that trigger rollup watch, will cause a source file not found error from rp2:

[!] (plugin rpt2) Error: Could not find source file: '/<path removed>/watch-err/source/lib/module1.ts'.
Error: Could not find source file: '/<path removed>/watch-err/source/lib/module1.ts'.
    at getValidSourceFile (/<path removed>/watch-err/node_modules/typescript/lib/typescript.js:153646:29)
    at Object.getSyntacticDiagnostics (/<path removed>/watch-err/node_modules/typescript/lib/typescript.js:153896:52)
    at /<path removed>/watch-err/node_modules/rollup-plugin-typescript2/src/index.ts:306:23
    at TsCache.getDiagnostics (/<path removed>/watch-err/node_modules/rollup-plugin-typescript2/src/tscache.ts:298:49)
    at TsCache.getSyntacticDiagnostics (/<path removed>/watch-err/node_modules/rollup-plugin-typescript2/src/tscache.ts:238:15)
    at /<path removed>/watch-err/node_modules/rollup-plugin-typescript2/src/index.ts:304:15
    at /<path removed>/watch-err/node_modules/rollup-plugin-typescript2/src/tscache.ts:183:61
    at arrayEach (/<path removed>/watch-err/node_modules/rollup-plugin-typescript2/node_modules/lodash/lodash.js:516:11)
    at Function._.each [as forEach] (/<path removed>/watch-err/node_modules/rollup-plugin-typescript2/node_modules/lodash/lodash.js:9368:14)
    at TsCache.walkTree (/<path removed>/watch-err/node_modules/rollup-plugin-typescript2/src/tscache.ts:183:4)

Repository with reproduction code

Steps to reproduce:

Run rollup -c rollup.config.js --watch
Trigger rollup watch by re-saving module2.ts or index.ts. Note that triggering watch with module1.ts will not produce the error.

I assume this is related to the directory structure of the project which uses baseUrl to point up to the “lib” dir. Also, I was not able to reproduce this without Vue.